tetra: an improved program for population genetic analysis of allotetraploid microsatellite data

Population genetic analysis of allotetraploid microsatellite data has lagged far behind that of diploid data, largely because of an inability to determine allele copy number for partial heterozygotes. tetrasat developed by Markwith et al. (2006) uses an iterative substitution process to account for all probable combinations of allele copy numbers in populations with partial heterozygote samples. However, tetrasat cannot deal with microsatellite data containing more than 15 partial heterozygotes, because of an exponential increase in genotype combinations. tetra can handle the microsatellite data containing infinite partial heterozygotes. In the program tetra, the frequencies of alleles are measured as the probability with which the known alleles occur in unknown allele locations. The Hardy–Weinberg expected heterozygosity and Nei's coefficient of gene differentiation are calculated based on allele frequencies. The mean and standard error of expected heterozygosity are estimated through bootstrap method.     

Principle of plotting the age distribution of persons with hereditary diseases at various ages of onset and differential mortality

A method for ascertaining the mode of current age distributions is suggested for accurate quantitative assessment of some genetic parameters of hereditary diseases, such as age-specific penetrance, frequency of heterozygotes in the general population, fitness. The method is based on estimating the age-specific proportion of affected among the total number of heterozygotes, which seems more reasonable than the common methodology, considering the age-specific proportion of affected among all cases of the disease indicated.     

Temporal genetic changes between cohorts in a natural population of a marine fish, Diplodus sargus

Temporal changes at 17 allozyme loci in the Diplodus sargus population of Banyuls sur Mer (Mediterranean Sea, France) were monitored within a single population among ten year‐classes (cohorts) sampled over a 6‐month period. The genetic survey was combined with evaluation of the demographic structure of the population by determining variation of abundance between cohorts. The population showed variation in abundance among cohorts ranging from 16 to 214 individuals. Significant divergences in genetic structure were observed between cohorts (P < 0.0001) despite very low values of F_ST (multilocus F_ST over all cohorts = 0.0018). The heterozygosity of each cohort, as well as the F_IS values, was significantly correlated with the abundance of each cohort, with abundant cohorts showing lower heterozygosity and a significant deficit of heterozygotes (positive F_IS values). Finally, multilocus temporal genetic variance (F_k) computed between successive cohorts was higher in low abundance cohorts. Change of heterozygosity between cohorts, distribution of year‐class genetic structure, and change in the genetic structure within a cohort appear to be affected mostly by the abundance of the cohort and are therefore driven by genetic drift. We propose that the Diplodus sargus cohorts are built up from the mixing of families during the pelagic stage or later during recruitment, and that the decrease in heterozygosity leading to a deficit of heterozygotes is characteristic of a Wahlund effect. Such a Wahlund effect would derive from the mixing of the progeny of families made up of few individuals, but exhibiting high fecundity and high variability of reproductive success. Therefore, although cohorts derived from poor recruitment would only group a few families and would exhibit limited deficit of heterozygotes (higher heterozygosity values), they would lead to high genetic drift and appear more divergent (higher mean temporal genetic variance) than cohorts with high abundance. While not demonstrating directly the family structure of marine populations, our survey provides evidence of highly structured populations. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 76 , 9–20.     

Heterozygosity for Tay-Sachs and Sandhoff diseases in non-Jewish Americans with ancestry from Ireland, Great Britain, or Italy

Previous reports have found that non-Jewish Americans with ancestry from Ireland have an increased frequency of heterozygosity for Tay-Sachs disease (TSD), although frequency estimates are substantially different. Our goal in this study was to determine the frequency of heterozygosity for TSD and Sandhoff diseases (SD) among Irish Americans, as well as in persons of English, Scottish, and/or Welsh ancestry and in individuals with Italian heritage, who were referred for determination of their heterozygosity status and who had no known family history of TSD or SD or of heterozygosity for these conditions. Of 610 nonpregnant subjects with Irish background, 24 TSD heterozygotes were identified by biochemical testing, corresponding to a heterozygote frequency of 1 in 25 (4%; 95% CI, 1/39-1/17). In comparison, of 322 nonpregnant individuals with ancestry from England, Scotland, or Wales, two TSD heterozygotes were identified (1 in 161 or 0.62%; 95% CI, 1/328-1/45), and three TSD heterozygotes were ascertained from 436 nonpregnant individuals with Italian heritage (1 in 145 or 0.69%; 95% CI, 1/714-1/50). Samples from 21 Irish heterozygotes were analyzed for HEXA gene mutations. Two (9.5%) Irish heterozygotes had the lethal + 1 IVS-9 G --> A mutation, whereas 9 (42.8%) had a benign pseudodeficiency mutation. No mutation was found in 10 (47.6%) heterozygotes. These data allow for a frequency estimate of deleterious alleles for TSD among Irish Americans of 1 in 305 (95% CI, 1/2517-1/85) to 1 in 41 (95% CI, 1/72-1/35), depending on whether one, respectively, excludes or includes enzyme-defined heterozygotes lacking a defined deleterious mutation. Pseudodeficiency mutations were identified in both of the heterozygotes with ancestry from other countries in the British Isles, suggesting that individuals with ancestry from these countries do not have an increased rate of TSD heterozygosity. Four SD heterozygotes were found among individuals of Italian descent, a frequency of 1 in 109 (0.92%; 95% CI, 1/400-1/43). This frequency was higher than those for other populations, including those with Irish (1 in 305 or 0.33%; 95% CI, 1/252-1/85), English, Scottish, or Welsh (1 in 161 or 0.62%; 95% CI, 1/1328-1/45), or Ashkenazi Jewish (1 in 281 or 0.36%; 95% CI, 1/1361-1/96) ancestry. Individuals of Irish or Italian heritage might benefit from genetic counseling for TSD and SD, respectively.     

Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift

Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population''s long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele''s presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population''s allele frequency spectrum to provide predictions for allele recovery. The model''s analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.     

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.     

Genetic counseling in carriers of reciprocal translocations involving two autosomes

One of the main genetic causes involve in the pathogenesis of recurrent abortion is parental chromosomal abnormalities. The central concept in genetic counseling with such families is to estimate the probability of recurrence of unfavorable pregnancy outcomes. The main questions that consultants usually ask are: Why did this happen? What is the risk to be done again?Our cases were two families with repeated miscarriage. The pedigrees were drawn, the chromosomes of couples were studied, and estimation for recurrent risk was done. We tried to answer those two main questions and clear the results for them.Parental chromosome abnormalities were founded after karyotyping with GTG technique at 450 band resolution, revealing 46 chromosomes with balanced translocation of autosomes in one of the partner in both families. Recurrent risk was estimated as “high” for their future pregnancies in each family.Couples in which one partner is the carrier of such balanced translocation have increased risks of infertility, recurrent abortion, and delivery of chromosomally abnormal offspring. Genetic counseling of such couples, therefore, presents a unique challenge and should be considered in dealing with such families.     

Historical habitat connectivity affects current genetic structure in a grassland species

Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co‐dominant markers to estimate genetic diversity and deviation from Hardy–Weinberg equilibrium in 31 populations distributed within a 5 km² agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale.     

Dynamics of allozyme heterozygosity in Siberian dwarf pine Pinus pumila (Pall.) Regel populations of the Russian Far East: comparison of embryos and maternal plants

Siberian dwarf pine, or Japanese stone pine, Pinus pumila (Pall.) Regel is widespread in eastern Siberia and the Russian Far East; the species is bird-dispersed and has a unique spreading or shrub living form. A mixed mating system (predominant outcrossing with self-pollination and matings of close relatives) leads to the formation of partly inbred progenies in P. pumila, as in the majority of other conifers. The question arises as to whether inbred individuals persist in the reproductive part of a population, which can have negative genetic consequences. The ADH, FDH, FEST, GDH, GOT, IDH, LAP, MNR, MDH, PEPCA, 6-PGD, PGI, PGM, SKDH, and SOD isozyme systems were analyzed to study the dynamics of heterozygosity in four P. pumila natural populations from the Pacific region, optimal for the species. Samples were collected in northern Koryakia, southern Kamchatka (two samples), and the Kunashir Island (Kurils). Wright's fixation index was used to estimate the level of inbreeding in embryos from dormant seeds resulting from free pollination and in maternal plants. A substantial level of inbreeding (F(IS) = 0.124-0.342) was observed in the embryo samples but not in three out of the four adult samples. The inbreeding level at the reproductive age was high only in the sample from Koryakia, which was explained by a relatively young age of plants in the population frequently affected by fires. A general increase in heterozygosity, characteristic of other conifers as well, was attributed to elimination of inbred progenies and by balancing selection for heterozygotes, which is a key factor maintaining allozyme polymorphism in populations.     

A primer for predicting risk of disease in HFE-linked hemochromatosis

Since the discovery of the hemochromatosis gene (HFE) in 1996, there has been increasing interest in diagnostic testing for the C282Y and H63D mutations. The high frequency of these two alleles and their incomplete penetrance in homozygotes and compound heterozygotes make genetic counseling for hemochromatosis different from some other autosomal recessive conditions in that parents and children may also be at risk for iron overload, while homozygotes may remain asymptomatic. We provide a guideline for genetic counseling in HFE-linked hemochromatosis based on the genetic probability of inheriting HFE mutations and known information about expression of iron overload in various HFE genotypes. Genetic probabilities were based on allele frequencies derived from large population studies and Hardy-Weinberg equilibrium estimates. Expression of iron overload in those of various genotypes was based on available estimates of serum ferritin from population screening studies. Estimates for the likelihood of clinical iron overload requiring follow-up screening or treatment are provided by gender and genotype. The probability of inheriting HFE mutations and developing iron overload can be estimated in family members of a proband with HFE mutations. Many C282Y homozygotes will not have clinical iron overload. The risk is highest in men and their C282Y homozygous brothers and significantly lower in homozygous women. Iron overload is uncommon in compound heterozygotes and H63D homozygotes.     

Genetic analysis of the predisposition to uterine myoma. Prevalence and morbidity

Prevalence of uterine myoma (MU) was estimated in several Moscow districts. The overall average estimate of the MU prevalence is 2.45% among women of all groups. The prevalence MU estimates increase with the age, its maximum value reaching 8.31% at the age of 50 years. The morbidity risk estimates increased with the age as well, the maximum value being 2.98% at the age of 40-44 years. The value of "cumulative" morbidity risks, i. e. the probability to be affected, is 9.74% for a population living long enough, this value being based on the age-specific estimates of morbidity risks. Taking into consideration the autopsy data, indicating that frequency of MU, including small myomatous nodes, is 20%, the conclusion is made that MU is manifested by clinically expressed disturbances (urging a woman to address to a doctor) in 50% of cases only. Epidemiological data obtained are to be used later for genetic analysis of familial data on MU.     

HETEROZYGOSITY AND DEVELOPMENTAL RATE IN A STRAIN OF RAINBOW TROUT (SALMO GAIRDNERI)

Rainbow trout (Salmo gairdneri) with greater heterozygosity at enzyme loci also have greater developmental stability, as measured by bilateral symmetry of five meristic traits. Fish with increased amounts of liver phosphoglucomutase activity have greater developmental stability and develop faster than fish with normal activity. These observations suggest that the differences in developmental stability between homozygotes and heterozygotes may be the result of differences in developmental rate. Faster developmental rates are expected to decrease the probability of accidents during critical periods of development, resulting in a more stable or uniform phenotype. As indicated by differences in hatching time, heterozygotes tend to develop more rapidly than homozygotes. This association is not strongly expressed within families at any locus except Pgm1-t. However, heterozygotes for Mdh3,4 and Hex hatched significantly sooner than homozygotes in a population sample. These results suggest that differences in developmental rate between homozygotes and heterozygotes may account for the positive association between developmental stability and heterozygosity in rainbow trout.     

Haemolytic anaemia in Basenji dogs. 2. Partial deficiency of erythrocyte pyruvate kinase (PK; EC 2.7.1.40) in heterozygous carriers

Congenital nonspherocytic haemolytic anaemia (HA) in dogs of the Basenji breed is inherited as a simple, autosomal recessive trait. Previous results of pyruvate kinase (PK) assays suggest a causal relationship between the anaemia and PK deficiency in erythrocytes. In the present investigation assays of this enzyme have been performed on haemolysates from 45 Basenji dogs, comprising 3 anaemic and 42 non-anaemic individuals of which 13 were known heterozygotes. The PK activity in haemolysates from the 42 non-anaemic dogs exhibited a bimodal distribution corresponding to the genotypic classes: heterozygotes and normal homozygotes. The results indicate that heterozygotes have a partial, detectable enzyme deficiency, not reflected in clinical disease, and thus give evidence of a gene dosage effect in agreement with observations in man. The proposed genotypes PK PK, PK pk and pk pk refer to normal homozygotes, heterozygotes, and anaemic individuals, respectively. The findings strengthen the genetic hypothesis of recessiveness of the anaemia by direct detection of heterozygosity of parents of affected individuals. Moreover, the results are of value in comparative studies and they have practical application in connection with eradication programmes.     

Humangenetische Beratung

With the increasing possibilities of genetic testing in clinical practice, genetic counseling becomes more and more important. Such counseling involves an attempt to answer questions and solve problems in connection with a possible genetic disorder. Reasons for genetic counseling are, among others, a possible genetic disorder in a child, a parent or a relative, advanced parental age, consanguinity, multiple pregnancy loss, stillbirths, infertility, and possible mutagenic or teratogenic exposure. Prenatal diagnosis, predictive and heterozygosity testing may have implications which differ from those of conventional diagnoses in medicine. The decision for testing should be made informed after genetic counseling. An overview of the aims, practical aspects and possible reasons for genetic counseling is provided.     

Population genetics of Fomitopsis rosea– a wood-decay fungus of the old-growth European taiga

The genetic structure of the wood-decay fungus Fomitopsis rosea (Alb. et Schw. Fr.) Karst is presented for populations sampled in Russia, Sweden and Finland. A total of 11 variable arbitrary primed (AP)–PCR markers were found to be segregated in a 1:1 ratio. The genotype for each fruiting body was inferred from the genotypes of the haploid single-spore isolates. Observed heterozygosity was lowest in southern Fennoscandia, the area with the longest history of forestry management. Overall, there was a deficit of heterozygotes compared with frequencies of heterozygotes predicted from Hardy–Weinberg expectations. When we partitioned the deficit of heterozygotes into the hierarchical genetic structure by means of F -statistics we found that the possible causes for it were both limited gene flow between regions and local nonrandom mating within all populations. Future management for the conservation of F. rosea populations and how the results relate to the life cycle of basidomycete fungi are discussed.     

Estimates of conditional heterozygosity risks for young females in Duchenne muscular dystrophy

Using the data from daughters of known carriers and from age-paired controls, we present a method for estimating the mean and variance of creatine kinase (CK) and pyruvate kinase (PK) in pre-menarchal and early adolescent Duchenne muscular dystrophy (DMD) carriers. CK and PK means and variances were estimated for different age ranges; it is shown that among DMD carriers the levels of both enzymes decrease linearly with age. A discriminant analysis was further performed for the estimation of biochemical risks favouring the diagnosis of heterozygosity for possible young carriers. The use of this method may also be applicable for other X-linked conditions in which the detection of heterozygotes is probabilistic.     

Utility and efficiency of linked marker genes for genetic counseling. II. Identification of linkage phase by offspring phenotypes

For a linked marker locus to be useful for genetic counseling, the counselee must be heterozygous for both disease and marker loci and his or her linkage phase must be known. It is shown that when the phenotypes of the counselee's previous children for the disease and marker loci are known, the linkage phase can often be inferred with a high probability, and thus it is possible to conduct genetic counseling. To evaluate the utility of linked marker genes for genetic counseling, the accuracy of prediction of the risk for a prospective child with a given marker gene to develop the genetic disease and the proportion of families in which a particular marker locus can be used for genetic counseling are studied for X-linked recessive, autosomal dominant, and autosomal recessive diseases. In the case of X-linked genetic diseases, information from children is very useful for determining the linkage phase of the counselee and predicting the genetic disease. In the case of autosomal dominant diseases, not all children are informative, but if the number of children is large, the phenotypes of children are often more informative than the information from grandparents. In the case of autosomal recessive diseases, information from grandparents is usually useless, since they show a normal phenotype for the disease locus. If we use information on the phenotypes of children, however, the linkage phase of the counselee and the risk of a prospective child can be inferred with a high probability. The proportion of informative families depends on the dominance relationship and frequencies of marker alleles, and the number of children. In general, codominant markers are more useful than are dominant markers, and a locus with high heterozygosity is more useful than is a locus with low heterozygosity.     

Evaluation of the genetic variability of 13 microsatellite markers in native Indian pigs

We analysed polymorphism of 13 microsatellites in two Indian domesticated pig types (North Indian and Northeast Indian). Heterozygosity, polymorphism information content, and probability of identity of two random individuals were calculated for all microsatellites in both types. The number of alleles observed at a locus varied between five and 12. The evaluated microsatellites exhibited a very high heterozygosity and polymorphism information content. The probability of identity of two random individuals from different populations taking into account all the 13 microsatellites was as low as 3.51 × 10^-19. On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying the genetic diversity and for identification of individuals in Indian pig types.     

Adult survival and microsatellite diversity in possums: effects of major histocompatibility complex-linked microsatellite diversity but not multilocus inbreeding estimators

Adult survival is perhaps the fitness parameter most important to population growth in long-lived species. Intrinsic and extrinsic covariates of survival are therefore likely to be important drivers of population dynamics. We used long-term mark-recapture data to identify genetic, individual and environmental covariates of local survival in a natural population of mountain brushtail possums (Trichosurus cunninghami). Rainfall and intra-individual diversity at microsatellite DNA markers were associated with increased local survival of adults and juveniles. We contrasted the performance of several microsatellite heterozygosity measures, including internal relatedness (IR), homozygosity by loci (HL) and the mean multilocus estimate of the squared difference in microsatellite allele sizes within an individual (mean d ²). However, the strongest effect on survival was not associated with multilocus microsatellite diversity (which would indicate a genome-wide inbreeding effect), but a subset of two loci. This included a major histocompatibility complex (MHC)-linked marker and a putatively neutral microsatellite locus. For both loci, diversity measures incorporating allele size information had stronger associations with survival than measures based on heterozygosity, whether or not allele frequency information was included (such as IR). Increased survival was apparent among heterozygotes at the MHC-linked locus, but the benefits of heterozygosity to survival were reduced in heterozygotes with larger differences in allele size. The effect of heterozygosity on fitness-related traits was supported by data on endoparasites in a subset of the individuals studied in this population. There was no apparent density dependence in survival, nor an effect of sex, age or immigrant status. Our findings suggest that in the apparent absence of inbreeding, variation at specific loci can generate strong associations between fitness and diversity at linked markers.