Genetic variation versus recombination rate in a structured population of mice

The correlation between genetic variation and recombination rate was investigated in a structured mouse population. Nucleotide sequence data from 19 autosomal DNA loci from eight inbred strains of mouse (Mus musculus) sampled from three major subspecies were analyzed. The recombination rate was estimated from the comparison of genetic and physical map distances between markers flanking a 10-cM region of each locus. The strains were categorized into four groups (subpopulations) based on geography. By partitioning the genetic diversity into within-group and among-group variation, we detected a positive correlation between the recombination rate and nucleotide diversity within groups. The level of nucleotide differentiation among groups (G(ST)) showed a negative correlation with the rate of recombination. There was no significant correlation between recombination rate and nucleotide diversity when data from different subpopulations were pooled. No correlation was detected between recombination rate and nucleotide divergence of M. musculus and M. spicilegus. These patterns deviate from the strict neutral expectation under the constant nucleotide substitution rate, and they are likely to have been formed either by a hitchhiking effect of positively selected mutants or by background selection of deleterious mutants occurring in a subdivided population. Our series of comparisons show that because a real population always has some structure, incorporation of its information is important in detecting non-neutral evolution.     

A simulation program based on a structured population model for biotechnological yeast processes

Summary A segregated population model for budding yeasts and a simulation program based on it are presented. They enable the study of bioprocesses utilizing yeasts in steady and perturbed conditions and in particular the comparison between the model predictions and the experimental results obtained by flow cytometry, which allows the measurement of segregated parameters of cell populations.Nomenclature a genealogical age - A parameter of the budding law - CV coefficient of variation - F _in(t) volumetric input flow - F _out(t) volumetric output flow - h parameter of the division law - K _s parameter of the Monod's law - m cell mass - M _i discretized cell mass - m _b (a,s) critical mass level for budding - m _p cell mass at the time of budding - n(t) cell number per unit volume - n _p number of sub-populations - n _c number of channels - p (a, i, j, k) discrete density function - Q parameter of the budding law - s(t) substrate concentration - S _in(t) substrate concentration in the input flow - t time - T _m minimal length of the budded phase - V(t) culture volume - x(t) biomass concentration - Y yield coefficient - channel width - (s) specific growth rate - _max parameter of the Monod's law     

Variance and covariance of homozygosity in a structured population

The variance of homozygosity for a K-allele model with n partially isolated subpopulations is derived numerically using identity coefficients. The variance of homozygosity within a subpopulation is shown to depend strongly upon the migration rates between subpopulations but is not strongly influenced by the number of alleles possible at a locus. The variance of homozygosity within a subpopulation, given the value of expected homozygosity, is approximately equal to the value of the variance of homozygosity given by Stewart's formula for a single population. If the population is presumed to be panmictic, but is actually subdivided, and the gametes are sampled at random from the total population, the apparent variance of homozygosity depends on the number of alleles possible. With small migration rates and K large, the apparent variance of homozygosity is much smaller than in a single population with the same expected homozygosity. However, when K is small, the variance of homozygosity is approximately given by Stewart's formula. The transient behavior of the variance of homozygosity shows that a large number of generations may be required to approach equilibrium values.     

Genetic disorders in children and young adults: a population study.

The data base of an ongoing population-based registry with multiple sources of ascertainment was used to estimate the present population load from genetic disease in more than 1 million consecutive live births. It was found that, before approximately age 25 years, greater than or equal to 53/1,000 live-born individuals can be expected to have diseases with an important genetic component. This total was composed of single-gene disorders (3.6/1,000), consisting of autosomal dominant (1.4/1,000), autosomal recessive (1.7/1,000), and X-linked recessive disorders (0.5/1,000). Chromosomal anomalies accounted for 1.8/1,000, multifactorial disorders (including those present at birth and those of onset before age 25 years) accounted for 46.4/1,000, and cases of genetic etiology in which the precise mechanism was not identified accounted for 1.2/1,000. Previous studies have usually considered all congenital anomalies (ICD 740-759) as part of the genetic load, but only those judged to fit into one of the above categories were included in the present study. Data for congenital anomalies are therefore also presented separately, to facilitate comparison with earlier studies. If all congenital anomalies are considered as part of the genetic load, then greater than or equal to 79/1,000 live-born individuals have been identified as having one or other genetic disorder before approximately age 25 years. These new data represent a better estimate of the genetic load in the population than do previous studies.     

Travelling wave dynamics and self-organization in a spatio-temporally structured population

We analyse spatial population dynamics showing that periodic or period-like chaotic dynamics produce self-organization structures, such as travelling waves. We suggest that self-organized patterns are associated with spatial synchrony patterns that often depend on geographical distance between subpopulations. The population dynamics also show statistical spatial autocorrelation patterns. We contrast our theoretical simulations with empirical data on annual damages in young sapling stands caused by voles. We conclude, on the basis of the periodicity, synchrony, and spatial autocorrelation patterns, and our simulation results, that vole dynamics represent travelling waves in population dynamics. We suggest that because such synchrony patterns are frequently observed in natural populations, spatial self-organization may be more common in population dynamics than reported in the literature.     

Genetic data on Alghero population (Sardinia): Contrast between biological and cultural evidence

Data on 20 genetic polymorphisms (61 alleles) in the Algehero population on the northwestern coast of Sardinia are presented and discussed in relation to its linguistic peculiarity inside the island. Since the Aragonese (Spain) conquest of Sardinia in the 13th century, the Catalan language, the same as that spoken in Northeastern Spain and certain districts of Southern France, has been used in Alghero even until today. Analysis for heterogeneity of gene frequency distributions indicates that the genetic information obtained on Alghero is adequate to discriminate Sardinians from other neighbouring populations. Genetic variation between populations measured through genetic distances and principal-component analysis shows that the present-day population of Alghero is much closer genetically to Sardinians than to Catalonians. Our genetic results do not support any interpretation of the linguistic affinities between Alghero and Catalonia at present as indicative of biological kinship. © 1994 Wiley-Liss, Inc.     

Genetic data for 15 STR loci in a Kadazan-Dusun population from East Malaysia

Allele frequencies of 15 short tandem repeat (STR) loci, namely D5S818, D7S820, D13S317, D16S539, TH01, TPOX, Penta D, Penta E, D3S1358, D8S1179, D18S51, D21S11, CSF1PO, vWA, and FGA, were determined for 154 individuals from the Kadazan-Dusun tribe, an indigenous population of East Malaysia. All loci were amplified by polymerase chain reaction, using the Powerplex 16 system. Alleles were typed using a gene analyzer and the Genemapper ID software. Various statistical parameters were calculated and the combined power of discrimination for the 15 loci in the population was calculated as 0.999999999999999. These loci are thus, informative and can be used effectively in forensic and genetic studies of this indigenous population.     

Similarity measures for structured data: a general framework and some applications to vegetation data

Although there are many measures of similarity existing in the phytosociological literature, these almost all apply to data for which the describing attributes have only single values. In many cases, however, there can be a richer structure in the attribute values, either directly from the nature of the attributes or derived from relationships between the stands. In this paper, I first examine a range of possible sources of such structure in phytosociological data, and then propose a similarity measure sufficiently general to be applicable to all the variant types. Finally I present some examples of applying such measures to frequency data from tropical grasslands and to successional data from subtropical rain forest.     

Genetic studies on Gadaba: a tribal population of Andhra Pradesh, India.

Blood samples were collected from Gadaba, a tribal population of Andhra Pradesh, South India, in order to examine the distribution of blood groups, red cell enzymes and the gammaglobulin polymorphism. Out of 20 genetic markers studied seven protein loci exhibited monomorphism. Surprisingly a case of a rare homozygous variant and twenty-one heterozygous variants at the phosphogluconate dehydrogenase locus (6-PGD), six variants at the phosphohexose isomerase locus (PHI) and a single case of phosphoglucomutase locus 1 (PGM 1) variant were observed. Further, the tribal populations of South India reveal higher frequencies of rare variants than the caste populations. However, the presence of rare variants that are phenotypically neutral may be plausibly due to their high selective value.     

Invasion and persistence of plant parasites in a spatially structured host population

Spatial structure is of central importance in the dynamics of plant-parasite interactions and is imposed by the growth habit and distribution of host plants and by parasite dispersal which is frequently restricted. To investigate the effects of spatial heterogeneity on the dynamics of plant parasites we introduce a simple model for epidemic development within a spatially structured host population. Here the host population is subdivided into a number of patches which are linked to allow for transmission from one patch to another with the connections defining the spatial structure of the host population. Three key parameters are identified that play a critical role in the ability of the parasite to invade and persist within the host population: the within-patch parasite basic reproductive number which characterises the infection dynamics at the local spatial scale; and the neighbourhood of interaction which describes which patches interact with which and the strength of coupling between patches within the neighbourhood which together characterise the spread of the parasite over larger spatial scales. Using both deterministic and stochastic formulations of the model, we investigate how the thresholds and probabilities of invasion and persistence are affected by these parameters, by demographic stochasticity and by differences in the initial level of infection.     

Genetic data on 15 STR loci in the Caucasian population of the Russian Federation

Population genetic data for the 15 STR loci included in the AmpFlSTR Identifier kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) obtained from 1118 unrelated Caucasian individuals from the Russian Federation are presented. In addition, a number of forensically useful genetic parameters are reported.     

Genetic and constitutional influences on serum-uric-acid in a tropical rural population

Summary The concentration of serum-uric-acid (S.U.A.) was determined by a colorimetric method in 1010 male subjects from northern Thailand (710 recruits, 300 prisoners). S.U.A. levels were compared with several constitutional and genetic factors. Body-weight, glucose-6-phosphate dehydrogenase deficiency and haemoglobin E do not seem to influence S.U.A. concentration in this population. Blood-group A and low S.U.A. levels were associated in recruits and prisoners under 25 years, but not in those over 25 years old. There was a strong association between low S.U.A. concentration and the presence of a thalassaemia gene ( or variety) or increased osmotic resistance of the erythrocytes. This is probably an expression of the known positive correlation between the concentrations of S.U.A. and circulating haemoglobin.

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Zusammenfassung Die Konzentration der Harnsäure im Serum (S.U.A.) wurde bei 1010 Männern aus Nord-Thailand (710 Rekruten; 300 Strafgefangenen) mit Hilfe einer kolorimetrischen Methode bestimmt. Die S.U.A.-Werte wurden mit verschiedenen konstitutionellen und genetischen Parametern verglichen. Körpergewicht, Glucose-6-Phosphat-Dehydrogenasemangel und Hämoglobin E scheinen in dieser Bevölkerung den S.U.A.-Wert nicht zu beeinflussen. Dagegen zeigte sich bei Rekruten und Strafgefangenen unter 25 Jahren eine Beziehung zwischen niedrigem S.U.A.-Wert und Blutgruppe A. Bei Personen über 25 fand sich diese Beziehung nicht. Außerdem fand sich eine engere Beziehung zwischen niedriger S.U.A.-Konzentration und der Anwesenheit eines Thalassämie-Gens (- oder -Typ) oder osmotischer Resistenz der Erythrocyten. Das ist wahrscheinlich, eine Folge der bekannten positiven Korrelation zwischen S.U.A.-Konzentration und zirkulierendem Hämoglobin.

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Established and supported by Stiftung Volkswagenwerk, Hannover, Germany.     

Genetic polymorphism of alpha-2-HS-glycoprotein in a Spanish population.

The genetic polymorphism of alpha-2-HS-glycoprotein (AHSG) was analyzed in 489 unrelated individuals living in Madrid (central Spain), by isoelectric focusing in miniaturized polyacrylamide gels followed by immunoblotting. The allele frequencies were estimated to be 0.7147 and 0.2771 for AHSG*1 and AHSG*2, respectively. In addition to the common alleles, 3 rare variants (AHSG*3, AHSG*10 and AHSG*11) have been found in this study.     

Genetic neighbourhood structure in a population of Picea abies L.

Summary Natural populations are currently the basic material for studying forest tree breeding, but little is known on the genotypic spatial structures in these stands. The use of gene markers, such as isozymes, leads to the determination of part of the allelic constitution of individuals. A method is presented here to estimate the degree of genetic relationship between any pair of genotypes. A French Picea abies population is analyzed by these means and a slight but significant correlation between estimated genetic relationship and topographic distance is found.     

The evolution of parasite virulence and transmission rate in a spatially structured population

If the transmission occurs through local contact of the individuals in a spatially structured population, the evolutionarily stable (ESS) traits of parasite might be quite different from what the classical theory with complete mixing predicts. In this paper, we theoretically study the ESS virulence and transmission rate of a parasite in a lattice-structured host population, in which the host can send progeny only to its neighboring vacant site, and the transmission occurs only in between the infected and the susceptible in the nearest-neighbor sites. Infected host is assumed to be infertile. The analysis based on the pair approximation and the Monte Carlo simulation reveal that the ESS transmission rate and virulence in a lattice-structured population are greatly reduced from those in completely mixing population. Unlike completely mixing populations, the spread of parasite can drive the host to extinction, because the local density of the susceptible next to the infected can remain high even when the global density of host becomes very low. This demographic viscosity and group selection between self-organized spatial clusters of host individuals then leads to an intermediate ESS transmission rate even if there is no tradeoff between transmission rate and virulence. The ESS transmission rate is below the region of parasite-driven extinction by a finite amount for moderately large reproductive rate of host; whereas, the evolution of transmission rate leads to the fade out of parasite for small reproductive rate, and the extinction of host for very large reproductive rate.     

Esterase D: some population and formal genetical data.

562 healthy blood donors and 65 families with 149 offspring were types for esterase D (EsD). The observed allele frequencies are in good agreement with those determined in other Caucasian populations. The rare variant EsD3 was found in a blood donor who transmitted it to his daughter. The observed segregation ratios in our family material showed no deviation from expectation.     

Genotoxic damage in polychaetes: a study of species and cell-type sensitivities

The marine environment is becoming increasingly contaminated by environmental pollutants with the potential to damage DNA, with marine sediments acting as a sink for many of these contaminants. Understanding genotoxic responses in sediment-dwelling marine organisms, such as polychaetes, is therefore of increasing importance. This study is an exploration of species-specific and cell-specific differences in cell sensitivities to DNA-damaging agents in polychaete worms, aimed at increasing fundamental knowledge of their responses to genotoxic damage. The sensitivities of coelomocytes from three polychaetes species of high ecological relevance, i.e. the lugworm Arenicola marina, the harbour ragworm Nereis diversicolor and the king ragworm Nereis virens to genotoxic damage are compared, and differences in sensitivities of their different coelomic cell types determined by use of the comet assay. A. marina was found to be the most sensitive to genotoxic damage induced by the direct-acting mutagen methyl methanesulfonate (MMS), and showed dose-dependent responses to MMS and the polycyclic aromatic hydrocarbon benzo(a)pyrene. Significant differences in sensitivity were also measured for the different types of coelomocyte. Eleocytes were more sensitive to induction of DNA damage than amoebocytes in both N. virens and N. diversicolor. Spermatozoa from A. marina showed significant DNA damage following in vitro exposure to MMS, but were less sensitive to DNA damage than coelomocytes. This investigation has clearly demonstrated that different cell types within the same species and different species within the polychaetes show significantly different responses to genotoxic insult. These findings are discussed in terms of the relationship between cell function and sensitivity and their implications for the use of polychaetes in environmental genotoxicity studies.     

Genetic influences on plasma cytokine variation in a parasitized population

The soil-transmitted helminths are the most common helminthic infections, affecting about one-fourth of the world's population. There is a significant genetic component to susceptibility to infection with these organisms. Substantial changes in plasma cytokine levels are associated with helminthic infections, and there may be significant genetic components to this cytokine variation. Six plasma cytokine levels were assessed for 367 members of a single pedigree from the Jirel population of eastern Nepal. This population experiences moderate rates of infection with geohelminths. Sex, age, helminthic infection, infection with Giardia, and presence of a household latrine were considered as covariates in all analyses of the cytokine data. The analyses of the single Jirel pedigree revealed significant heritabilities for IFN-gamma (h2 = 0.654+/-0.096), TNF-alpha (h2 = 0.458+/-0.101), IL-2 (h2 = 0.583+/-0.101), IL-4 (h2 = 0.700+/-0.095), IL-5 (h2 = 0.676+/-0.087), and IL-10 (h2 = 0.597+/-0.093). The ratios of IL-4 to IFN-gamma and of IL-10 to IFN-gamma were used as indicators of the degree of type 2 bias in immunological response; analyses of these variables indicated that approximately 40-60% of the variation (h2 = 0.400-0.577) in these derived measures of relative type 2/type 1 response is due to genetic factors.     

Genetic variation and covariation in a population of tetraploid Dactylis L. accessions

Summary Efficient utilization of divergent germ plasm sources in breeding cultivated Dactylis glomerata L. ssp. glomerata Domin depends on knowledge of quantitative variation within and among accessions. This study was undertaken to quantify variation and covariation for forage yield, maturity, disease reaction, and ground cover within a population of tetraploid Dactylis accessions. Variation was observed among families within the population for each variable. Most genetic variation (73%–93% of the family sums of squares) was within country sources or within accessions. Thus, country boundaries, which are traditionally important factors used in defining limits of plant exploration expeditions, have limited expected use in targeting future exploration for specific sources of high yield, disease resistance, or ground cover. Maturity was the exception to this; late-maturing accessions were identified as originating exclusively from the USSR. Some relationships among traits, such as that for yield and disease reaction, differed for accessions and cultivars. Several accessions and families within accessions were identified to have performance superior to most or all cultivars included in this study. Existing germ plasm from several countries was identified to have potential in breeding orchardgrass, while that from other countries appeared to have little or no potential in supplying germ plasm for hay production in humid-temperate environments.