A method for adjusting allele frequencies in the case of microsatellite allele drop‐out

A new method is proposed to adjust allele frequencies when allelic drop‐out is common. This method assumes Hardy–Weinberg equilibrium (HWE), and treats the problematic alleles as a one‐locus two‐allele system with dominance. By assuming that the homozygote frequency of the ‘recessive’ allele is measured correctly, we can back calculate the allele frequency of the ‘dominant’ allele, and adjust the heterozygote frequency accordingly. The drawback is that multilocus genotypes cannot be constructed and tests that use deviations from Hardy–Weinberg such as tests for bottlenecks become impossible. An example is given where a large homozygote excess (F_IS = 0.44) is adjusted to a reasonable level (F_IS = 0.046). The effect of scoring error was set in relation to sampling error and while F_IS values can be seriously biased, F_ST values are not necessarily so, if scoring error and sample size are both low. As sample size increases, the effect of scoring error increases.     

A private allele ubiquitous in the Americas

The three-wave migration hypothesis of Greenberg et al. has permeated the genetic literature on the peopling of the Americas. Greenberg et al. proposed that Na-Dene, Aleut-Eskimo and Amerind are language phyla which represent separate migrations from Asia to the Americas. We show that a unique allele at autosomal microsatellite locus D9S1120 is present in all sampled North and South American populations, including the Na-Dene and Aleut-Eskimo, and in related Western Beringian groups, at an average frequency of 31.7%. This allele was not observed in any sampled putative Asian source populations or in other worldwide populations. Neither selection nor admixture explains the distribution of this regionally specific marker. The simplest explanation for the ubiquity of this allele across the Americas is that the same founding population contributed a large fraction of ancestry to all modern Native American populations.     

Non-equilibrium theory of the allele frequency spectrum

A forward diffusion equation describing the evolution of the allele frequency spectrum is presented. The influx of mutations is accounted for by imposing a suitable boundary condition. For a Wright-Fisher diffusion with or without selection and varying population size, the boundary condition is lim(x downward arrow0)xf(x,t)=thetarho(t), where f(.,t) is the frequency spectrum of derived alleles at independent loci at time t and rho(t) is the relative population size at time t. When population size and selection intensity are independent of time, the forward equation is equivalent to the backwards diffusion usually used to derive the frequency spectrum, but this approach allows computation of the time dependence of the spectrum both before an equilibrium is attained and when population size and selection intensity vary with time. From the diffusion equation, a set of ordinary differential equations for the moments of f(.,t) is derived and the expected spectrum of a finite sample is expressed in terms of those moments. The use of the forward equation is illustrated by considering neutral and selected alleles in a highly simplified model of human history. For example, it is shown that approximately 30% of the expected total heterozygosity of neutral loci is attributable to mutations that arose since the onset of population growth in roughly the last 150,000 years.     

Assessment of the FAM174A 11G allele as a risk allele for equine metabolic syndrome

An 11G nucleotide repeat in the 3′ UTR of FAM174A was recently postulated as a risk allele with a dominant mode of inheritance for equine metabolic syndrome (EMS) and laminitis status in Arabian horses. The objective of this project was to evaluate this hypothesis in a large and diverse across-breed population. A total of 301 ponies, 292 Morgans, 64 Arabians, 49 Tennessee Walking Horses and 59 Quarter Horses were genotyped for six observed G repeat alleles in the FAM174A 3′ UTR. Phenotype data included laminitis status, baseline insulin, glucose, non-esterified fatty acids, triglycerides, adiponectin, leptin, ACTH, insulin and glucose post oral sugar test, and two proxies for insulin resistance. The 11G allele frequencies were 18.8, 6.9, 1.8, 0.2 and 0.0% in the Arabians, Tennessee Walkers, ponies, Morgans and Quarter Horses respectively. Association analyses between FAM174A genotype and EMS phenotypes, and between allele count and EMS phenotypes, identified no statistically significant associations. When a dominant effect for the 11G allele was evaluated, a statistically significant association with adiponectin levels was identified in the ponies, and pairwise comparisons revealed that the estimated marginal means were higher in ponies with the 11G allele vs. alternative alleles (i.e. the allele had a protective effect). In conclusion, our data do not support the FAM174A 11G allele as a risk allele for EMS in our studied breeds.     

A self-compatible mutant S allele conferring a dominant negative effect on the functional S allele in Ipomoea trifida

A spontaneously occurring self-compatible mutant has been identified in Ipomoea trifida, a species possessing sporophytic self-incompatibility controlled by a single multiallelic S locus. Analysis of the segregation of compatibility/incompatibility phenotypes in selfed and crossed progenies of the self-compatible mutant plant indicated that the self-compatibility trait was caused by a mutation at the S locus; the mutated S allele was therefore designated Sc. RFLP analysis of progeny plants segregating for the Sc allele using the SSP gene (a gene linked closely to the S locus of I. trifida) as a probe confirmed that the mutation was present at the S locus. Self-incompatibility responses were examined in F₁ progenies obtained from crosses between the self-compatible mutant and self-incompatible plants homozygous for one of three S alleles, S ₁ , S ₃ and S ₂₂ , where the dominance relationship is S ₂₂ >S ₁ >S ₃ . All F₁ progeny plants from crosses with S ₂₂ and S ₁ homozygotes were self-incompatible and exhibited the respective phenotypes of each self-incompatible parent (either S ₂₂ or S ₁ ) in both stigma and pollen. However, of the F₁ progeny plants from the cross with the S ₃ homozygote, those carrying the genotype ScS ₃ were all self-compatible and cross-compatible as both female and male parents with the S ₃ homozygote. These results indicate that the dominance relationship between the four S alleles is: S ₂₂ >S ₁ >Sc>S ₃ and so reveal the unexpected finding that the mutated Sc allele is dominant over a functional S ₃ allele. A possible explanation for this observation is that the gene product encoded by the Sc allele confers a dominant negative effect on the S ₃ gene product. Received: 21 June 2000 / Accepted: 18 July 2000     

A note on the estimation of allele frequencies

A new method of obtaining allele frequency estimates is described. The method may prove useful when maximum likelihood estimates are not available. No assumptions regarding the absence of alleles are required. Errors of estimates have not been obtained, but the process seems to converge to maximum likelihood.     

Inheritance of the equine Tf F3 allele

The inheritance of the equine Tf F3 allele was examined in 39 parent-offspring combinations. For 26 of the cases the allele inherited by the offspring from the heterozygous parent could be determined. The proportion of individuals that inherited the F3 variant compared to the alternative allele was exactly 1:1. In five cases the parental phenotype was identical to that of the offspring. For the remaining eight cases the parent was homozygous for the F3 allele and all offspring had the F3 allele. The results were consistent with Mendelian inheritance.     

A third allele in the horse albumin system

Starch gel electrophoresis according to Gahne (1966) reveals three new phenotypes designated FI, I and IS in horse serum albumin. Family material comprising 97 sire families with a total number of 2742 foals and their dams and population material comprising 2867 adult horses representative of the Swedish Trotter breed were examined. The results were consistent with a genetic theory of three codominant, autosomal alleles F, I and S controlling the six albumin phenotypes observed. The gene frequencies were estimated to be 0.489, 0.049 and 0.462, respectively, for the F, I and S genes in the Swedish Trotter breed. The risk of making false exclusions in paternity controls in the albumin system, if the I allele is not considered, is discussed.     

Population frequency of the arylsulphatase A pseudo-deficiency allele

Summary The enzymatic diagnosis of metachromatic leukodystrophy is complicated by the frequent occurrence of the pseudo-deficiency of arylsulphatase A (ASA) enzyme activity. An A to G nucleotide transition in the first polyadenylation signal of the ASA gene results in the loss of its major mRNA species and a greatly reduced level of enzyme activity. This nucleotide change (nucleotide 1620 of the ASA cDNA) is the cause of ASA pseudo-deficiency and is closely linked to another A to G transition (nucleotide 1049), within the ASA gene, which changes Asn₃₅₀ to serine but which does not affect ASA activity. The distribution of these 2 nucleotide changes has been investigated in 73 unrelated individuals from the Australian population. The two transitions were found together on 14 (9.6%) out of 146 chromosomes. The transition at nucleotide 1620 was not found alone; however, the other transition was found alone on 7 (4.8%) out of the 146 chromosomes. The carrier frequency of the ASA pseudo-deficiency mutation in Australia is thus estimated to be about 20%.     

Reconstitution of the R compound allele in maize

The R^r:standard allele in maize, which conditions anthocyanin pigmentation in plant and seed tissues in the presence of appropriate complementary factors, is associated with a tandem duplication. The proximal member of the duplication carries P, the plant pigmenting determiner and the distal member member carries S, the seed pigmenting determiner. Derivatives from R^r that have lost S function are designated r^r. They represent either losses of the distal member of the duplication (P derivatives) or mutations of S to s (P s). Derivatives that have lost P function are designated R^g, and represent either losses of the proximal member of the duplication (S derivatives) or mutations of P to p (p S).—All four possible types of r^r/R^g heterozygotes were tested for their capacity to yield R^r reconstitution by crossing over. No R^r derivatives were obtained from P/S heterozygotes, a result consistent with the view that P and S occupy corresponding positions in homologous chromosome segments. R^r reconstitution was detected in both tandem duplication heterozygotes P s/S and P/p S, and was found to be about ten times more frequent in the latter. The ratio of R^r reconstitution in the two heterozygotes is a function of position of the anthocyanin marker within the duplicated segment. The data from these heterozygotes allow one to measure the distance between P and S, that is to say, the genetic length of the duplicated segment. This distance was found to be 0.16 map units. The highest frequency of R^r reconstitution was obtained from P s/p S heterozygotes, since direct pairing (see PDF) as well as the p//s type of displaced pairing have the potential to produce R^r derivatives. One of the R^g derivatives used in this study, R^g₆, was found to back-mutate in some sublines to R^r. The basis for this instability remains unknown.     

Glyoxalase I 'null' allele in the Polish population

A silent allele of red-cell glyoxalase I was found in three generations of a Polish family.     

Confirmation of linkage disequilibrium between haplotype B (XV-2c,allele 1; KM-19, allele 2) and cystic fibrosis allele in the French population

Summary In 237 French families with cystic fibrosis (CF) restricted fragment length polymorphisms (RFLPs) were detected by two DNa probes, XV-2c and KM-19, which are tightly linked to the CF allele. As in other European populations linkage disequilibrium is found between the haplotype B (XV-2c, allele 1: KM-19, allele 2) and the CF allele. Linkage disequilibrium alters the probability that a person bearing a given haplotype is a carrier.     

Estimating the time since the fixation of a beneficial allele

The fixation of a beneficial allele in a population leaves a well-characterized signature in patterns of nucleotide variation at linked sites. This signature can be used to estimate the time since fixation from patterns of polymorphism in extant individuals. I introduce a method to assess the support in polymorphism data for a recent episode of directional positive selection and to estimate the time since fixation. I summarize the polymorphism data by three statistics that carry information about levels of diversity, the allele frequency spectrum, and the extent of allelic associations. Simulations are then used to obtain a sample from the posterior distribution of the time since fixation, conditional on the observed summaries. I test the performance of the approach on simulated data and apply it to the gene tb1 in maize. The data support the recent fixation of a favored allele, consistent with what is known about the importance of tb1 in the domestication process of maize.     

A new allele of the lurcher gene, lurcher

A new neurological mouse mutation that arose spontaneously in a BALB/cByJ stock displays a semidominant pattern of inheritance. In the heterozygote, this mutation results in an early loss of Purkinje cells in the cerebellum, which is followed by the overt symptom of an ataxic gait first observed at postnatal day 13 (P13). A portion of animals homozygous for the mutation die within P0; the remaining homozygotes die by P25. The mutation maps to mouse Chromosome (Chr) 6 between markers D6Rck314 and D6Rck361, a chromosomal segment that contains the lurcher (Lc) locus. The Lc mutation is also semidominant and has a strikingly similar phenotype. A cross between a new mutant (Nm) heterozygote and an Lc heterozygote yields double heterozygotes, animals that carry both mutations, with a phenotype similar to that of both Nm and Lc homozygotes. The similarity in phenotype, the colocalization of the two loci on mouse Chr 6, and the positive result of the allelism test demonstrate that the new mutation is an allele of the Lc gene. Received: 4 April 1997 / Accepted: 21 April 1997