The distribution of individual heterozygosity in natural populations

Estimation of the distribution of the level of individual heterozygosity within natural populations is explored with both Monte-Carlo simulation studies and data from natural populations. Simulations indicate that heterozygosities estimated from as few as a dozen randomly chosen loci may, to some degree, reflect (r = 0.35) heterozygosity determined by 100 independent loci. The shape of the expected distribution of heterozygosity is heavily dependent upon levels of heterozygosity at the loci. Complete genetic data for 12 loci from 997 Fundulus heteroclitus are used to describe the distributions of heterozygosity for different localities, for age classes and for sexes. The distributions deviate from normality. Distributions from different localities are not different, but the distributions are heterogeneous among age classes at one of two localities and are heterogeneous between the sexes.     

Heterozygosity-fitness correlations in a bottlenecked island species: a case study on the Seychelles warbler

We used capture-mark-recapture models to investigate the effects of both individual and parental heterozygosity, measured at microsatellite loci on the survival of Seychelles warblers (Acrocephalus sechellensis), an endemic island species which went through a severe population bottleneck in the middle of the last century. We found that an individual's survival was not correlated with multilocus heterozygosity, or with heterozygosity at any specific locus. However, maternal, but not paternal, multilocus heterozygosity was positively associated with offspring survival, but only in years with low survival probabilities. A nestling cross-fostering experiment showed that this was a direct maternal effect as there was an effect of the genetic mother's, but not of the social mother's, heterozygosity. Heterozygosity-fitness correlations at microsatellite markers were generally assumed to reflect genome-wide effects. Although this might be true in partially inbred populations, such correlations may also arise as a result of local effects with specific markers being closely linked to genes which determine fitness. However, heterozygosity at the individual microsatellite loci was not correlated and therefore does not seem to reflect genome-wide heterozygosity. This suggests that even in a small bottlenecked population, heterozygosity-fitness correlations may not be caused by genome-wide effects. Support for the local effects hypothesis was also equivocal; although three specific loci were associated with offspring survival, including all single-locus heterozygosities as independent predictors for the variation in survival was not supported by the data. Furthermore, in contrast to the local effects hypothesis, the loci which contributed most to the heterozygosity-survival relationship were not more polymorphic than the other loci. This study highlights the difficulties in distinguishing between the two hypotheses.     

The Effects of Heterozygosity Changes on Viability in DROSOPHILA MELANOGASTER

The viability effects of chromosomes from an old and from a new laboratory strain of D. melanogaster were studied in eight factorial combinations and at two heterozygosity levels. The combinations were so constructed that heterozygosity level could be varied in the third chromosomes of the carriers of a homozygous lethal marker, in the third chromosomes of their wild-type segregants, and in the genetic backgrounds of both. Excluding the effect of the marker and the exceptional outcomes of two of the combinations, and taking into account both large and small deviations from theoretical expectation, the following summary is given as the simplest consistent explanation of the results: 1) If total heterozygosities of two segregant types tend toward equality their viabilities tend toward equality also, whether background heterozygosity is high or low; if background heterozygosities is higher the tendency toward equality is slightly greater. 2) If total heterozygosity of two segregant types are unequal the less heterozygous type has the lower viability; the difference is more pronounced when background heterozygosity is low, less when it is high. 3) Differences between segregant viabilities are correlated with differences between the total heterozygosities of the two segregants; genetic background is effective to the extent, and only to the extent, that it contributes to the magnitude of this difference. This in turn appears to underlie, at least partly, the expression of a pronounced interchromosomal epistasis. Thus in this study viability is seen to depend upon both the quantity and distribution of heterozygosity, not only among the chromosomes of an individual but among the individuals of a given combination as well.     

Microsatellite DNA markers for the ground beetle Carabus insulicola

Twelve microsatellite DNA loci were newly isolated from the ground beetle Carabus insulicola, endemic to Japan, for studying mating systems. Phage vector was used for establishing genomic DNA library, and positive clones were screened with ³²P‐labelled probes. Primer sequences and annealing temperature for PCR amplification were determined for each locus. Allelic polymorphism of each locus, number of alleles and observed and expected heterozygosities, were investigated based on 24 individuals. Similarity between observed and expected heterozygosities suggests random mating, and relatively low observed heterozygosity found in two loci may be due to the presence of null alleles.     

Genetic variation in Australian Merino sheep

Variation at 22 gene loci was investigated in a flock of Australian Merino sheep using restriction fragment length polymorphism (RFLP) analysis. Polymorphism was observed at 20 loci, including loci for wool keratin, hormone and immunoglobulin light chain genes. Eleven loci yielded unambiguous genotypes suitable for population data analysis. Average heterozygosity, determined from these and two monomorphic loci, was estimated as 0.107 (SE = 0.024). Average heterozygosity excluding all monomorphic data was estimated as 0–377 (SE = 0.031), which is comparable with human RFLP heterozygosities for loci chosen in the same way that we selected sheep loci.     

Analysis of heterozygosity levels at P1,TF, PGM1, ACP1, HP, GC, GLO, C3, and ESD loci in pulmonary tuberculosis patients with different treatment outcomes]

Heterozygosity at nine genetic loci (PI, TF, PGM1, ACP1, HP, GC, GLO1, C3, and ESD) was analyzed in pulmonary tuberculosis patients with good (group 1, N = 71) and poor (group 2, N = 35) response to treatment. The observed heterozygosities were compared with the expected values, which were calculated from allele frequencies in a control sample of healthy individuals (N = 328 with all but one locus and 78 with ESD) according to Hardy-Weinberg expectations. The analysis showed that the observed heterozygosities gl of patients significantly differed from the expected values hl in the case of four loci (GC, PI, C3, and ACP1). The observed heterozygosity was higher than expected in three cases (PI, C3, and ACP1) and lower then expected (GC) in one case. When data on each individual locus were compared using Fisher's exact test, both groups of patients proved to significantly differ (PF < 0.05) from the control group in the same four loci. No difference in observed heterozygosity was detected between the two groups of patients. The mean expected heterozygosity was h = 0.386 +/- 0.00674; the mean observed heterozygosity was g = 0.415 +/- 0.02 in group 1, g = 0.402 +/- 0.026 in group 2, and g = 0.371 +/- 0.00955 in the control group. The t test did not reveal a significant difference between the mean values of expected observed heterozygosities. Heterozygosity at individual loci, rather than mean heterozygosity, was proposed as an integral nonspecific indicator of the genetic control of a disease, because the former directly implicates individual marker loci in the development of a disorder, whereas effects of individual loci may eliminate each other when mean heterozygosity is computed. Based on the results obtained, a genetic control was assumed for the development of the tuberculosis process in the lungs.     

STATISTICAL ANALYSIS OF HETEROZYGOSITY DATA: INDEPENDENT SAMPLE COMPARISONS

The distribution of mean heterozygosities under an infinite allele model with constant mutation rate was examined through simulation studies. It was found that, although the variance of the distribution decreases with increasing numbers of loci examined as expected, the shape of the distribution may remain skewed or bimodal. The distribution becomes symmetrical for increasing mean heterozygosity levels and numbers of loci. As a result, parametric statistical tests may not be valid for making comparisons among populations or species. Independent sample t-tests were examined in detail to determine the frequency of rejection of the null hypothesis when pairs of samples are drawn from populations with the same mean heterozygosity. Differing numbers of loci and levels of mean heterozygosity were examined. For mean heterozygosity levels above 7.5%, t-tests provide the proper rejection rate, with as few as five loci. When mean heterozygosity is as low as 2.5%, the t-test is conservative even when 40 loci are examined in each population. Independent sample t-tests were then examined for their power to detect true differences between populations as the degree of difference and number of loci vary. Although large differences can be found with high certainty, differences on the order of 5% heterozygosity may require that large numbers of loci (>40) be examined in order to be 80% or more certain of detecting them. In addition, it is emphasized that, for small numbers of loci (<25), the statistical detection of differences of interesting magnitude requires that relatively rare sampling events occur and that much larger differences be observed among the samples than exist for the population means. Two reasons exist for the lack of sensitivity of the test procedures. First, when mean heterozygosity levels are low, the non-normality of the sample means is perhaps most important. Second, even when mean heterozygosity levels are high or when sample sizes are large enough so sample means are approximately normally distributed, the intrinsically high interlocus variance of heterozygosity estimates makes the tests insensitive to the presence of heterozygosity differences that might be biologically meaningful. Finally, the implications of the results of this study are discussed with regard to observed low levels of correlation between heterozygosity and other explanatory variables.     

Isolation and characterization of polymorphic microsatellite loci from Brandt's voles (Lasiopodomys brandtii)

Ten polymorphic microsatellite loci from Lasiopodomys brandtii have been isolated and characterized. Two to 11 alleles per locus were detected from 52 Brandt's voles samples collected from a single population. Expected heterozygosities ranged from 0.406 to 0.840. For the majority of loci observed heterozygosities were similar to or greater than the expected heterozygosity. One locus pair appeared to be in linkage disequilibrium. The microsatellite markers will enable the studies of genetic diversity, population structure and relatedness in this species, and perhaps in closely related species of vole.     

High levels of genetic variation in natural populations of marine lower invertebrates

The predictions of neutralist and selectionist hypotheses have been tested many times in the past, but mostly using data only from organisms such as vertebrates, with generally low to average heterozygosities. The more recent discovery of particularly high levels of genetic variation in marine sponges and coelenterates provides an opportunity to use data from such species to contribute further to the understanding of the determinants of heterozygosity in natural populations. Therefore, 23 species of sponges and coelenterates from temperate, tropical and boreal waters were analysed by gel electrophoresis for an average of 14.3 enzyme loci per species. Mean heterozygosity values for each species were unusually high, ranging between 0.106 and 0.401. The means and variances of the heterozygosity estimates showed reasonable correlation with neutralist predictions (with both the stepwise mutation and the infinite alleles models). Population sizes were generally difficult to estimate with any confidence, but, for one sponge species for which this was possible, levels of heterozygosity again were similar to neutralist predictions, although the same was not apparently true for three species of sea anemone. No differences were found between heterozygosity levels of tropical and temperate species of sponges and coelenterates, thus apparently contradicting the selectionist ‘trophic resource stability’ and ‘temporal environmental variation’ hypotheses. Conversely, however, the consistently high levels of genetic variation found in coelenterates and sponges may be argued to be related to common biological characteristics, such as sessile life, great evolutionary ‘age’, limited ability to disperse and probable low homoeostatic capability. Our results seem, overall, to agree well with neutralist expectations for species with large, stable population sizes. Also, the mean heterozygosities, their variances and the observed and expected proportions of polymorphic loci seem to fit well with predictions based on the neutralist hypothesis. However, the selectionist ‘environmental grain’ and the ‘shifting balance’ hypotheses fit the data equally well. As with much earlier work, the problems in distinguishing between the various predictions of selectionist or neutralist ideas make it both difficult and unwise to draw definite conclusions.     

Heterozygosity-fitness correlations in a migratory bird: an analysis of inbreeding and single-locus effects

Studies in a multitude of taxa have described a correlation between heterozygosity and fitness and usually conclude that this is evidence for inbreeding depression. Here, we have used multilocus heterozygosity (MLH) estimates from 15 microsatellite markers to show evidence of heterozygosity-fitness correlations (HFCs) in a long-distance migratory bird, the light-bellied Brent goose. We found significant, positive heterozygosity-heterozygosity correlations between random subsets of the markers we employed, and no evidence that a model containing all loci as individual predictors in a multiple regression explained significantly more variation than a model with MLH as a single predictor. Collectively, these results lend support to the hypothesis that the HFCs we have observed are a function of inbreeding depression. However, we do find that fitness correlations are only detectable in years where population-level productivity is high enough for the reproductive asymmetry between high and low heterozygosity individuals to become apparent. We suggest that lack of evidence of heterozygosity-fitness correlations in animal systems may be because heterozygosity is a poor proxy measure of inbreeding, especially when employing low numbers of markers, but alternatively because the asymmetries between individuals of different heterozygosities may only be apparent when environmental effects on fitness are less pronounced.     

Can a simple algebraic analysis predict markers-genome heterozygosity correlations?

A current algebraic analysis on genome-wide heterozygosity estimates suggests that correlations between molecular markers and genome-wide heterozygosity, rho, depend on the ratio between the number of markers used, r, and the number of genome loci, n; that is: rho approximately square root r/n. Hence, it is unfeasible to obtain reliable estimates of genome-wide heterozygosity in species of large genome using a few markers. We cast some doubts about this analysis as it assumed that the probability that an individual was heterozygous at a locus is equal to the average heterozygosity of this locus in the population. However, we believe that individual heterozygosity at a given locus depends on individual pedigree. Because the pedigree is common for all loci of an individual, their probabilities of heterozygosity are not independent within the genome. We first performed simulations generating random genomes for 100 individuals. Among these individuals, markers and genome-wide heterozygosities correlated as expected from the above equation. However, when we simulated random mating among these individuals and in successive generations including their descendents, as occur in real populations, the correlations between markers and genome-wide heterozygosity were much higher than those predicted from algebraic analyses, and estimates of genome-wide heterozygosity improved slightly with the increment of the number of loci in the genome.     

Alternative Models for Allozyme-Associated Heterosis in the Marine Bivalve Spisula Ovalis

Correlations between allozyme heterozygosity and fitness-related traits, especially growth, have been documented in natural populations of marine bivalves. However, no consistent pattern has been exhibited, because heterotic effects on size vary with age and individual growth parameters are generally unknown. No consensus has emerged on the genetic basis of allozyme-associated heterosis. The species studied here, Spisula ovalis, displays annual shell growth lines, which allows us to compute individual age and growth dynamics over the whole life span. Our morphological study was coupled to a protein electrophoresis study at seven polymorphic loci. While the maximum size gained is not related to heterozygosity, the age at half maximum size, t(1/2), is significantly negatively correlated with heterozygosity, indicating an heterotic effect on initial growth. The correlation between heterozygosity and size is expected to vanish when age increases, due to the form of the growth function. This decreasing correlation is consistent with previous studies. We compare the relative performances of five linear models to analyze the genetic basis of heterosis. Surprisingly, the largest part of variance in t(1/2) is due to additive effects, the overdominant components being much weaker. Heterosis is therefore due to general genomic effects rather than to local overdominance restricted to allozymes or small neighboring chromosomal segments. A significant dependence of individual heterotic contributions of the enzyme loci upon expected heterozygosities, rather than metabolic function, further supports the hypothesis of enzymes acting as markers. General genomic effects can hold only if allozyme heterozygosity is positively correlated with heterozygosity at fitness-related genes scattered throughout the genome. This hypothesis is supported here by heterozygosity correlations between enzymatic loci.     

Development and characterization of 21 polymorphic microsatellite loci in the aphidophagous gall midge, <Emphasis Type="Italic">Aphidoletes aphidimyza</Emphasis> (Diptera: Cecidomyiidae)

We have developed and characterized 21 microsatellite markers in the aphidophagous gall midge Aphidoletes aphidimyza (Rondani) (Diptera: Cecidomyiidae). All 21 loci tested were polymorphic: the number of alleles ranged from 2 to 17. Allelic richness and observed heterozygosities were higher in females than in males. Several loci had no heterozygosity in males, suggesting that the loci were located on sex chromosomes or E-chromosomes, common to cecidomyiids. The high polymorphism detected in this study suggests the markers will be of value in analyzing genetic structure of field populations.     

Interrelationships of Heterozygosity, Growth Rate and Heterozygote Deficiencies in the Coot Clam, Mulinia Lateralis

Allozyme surveys of marine invertebrates commonly report heterozygote deficiencies, a correlation between multiple locus heterozygosity and size, or both. Hypotheses advanced to account for these phenomena include inbreeding, null alleles, selection, spatial or temporal Wahlund effects, aneuploidy and molecular imprinting. Previous studies have been unable to clearly distinguish among these alternative hypotheses. This report analyzes a large data set (1906 individuals, 15 allozyme loci) from a single field collection of the coot clam Mulinia lateralis and demonstrates (1) significant heterozygote deficiencies at 13 of 15 loci, (2) a correlation between the magnitude of heterozygote deficiency at a locus and the effect of heterozygosity at that locus on shell length, and (3) a distribution of multilocus heterozygosity which deviates from that predicted by observed single-locus heterozygosities. A critical examination of the abovementioned hypotheses as sources of these findings rules out inbreeding, null alleles, aneuploidy, population mixing and imprinting as sole causes. The pooling of larval subpopulations subjected to varying degrees of selection, aneuploidy or imprinting could account for the patterns observed in this study.     

Genetic variability and components of fitness in hatchery strains of rainbow trout

Two fitness components, development rate and egg size, were examined in six hatchery strains of rainbow trout, Oncorhynchus mykiss (syn. Salmo gairdneri Richardson), with different amounts of enzyme heterozygosity. The average expected heterozygosities per strain ranged from 4 to 8%, based upon an electrophoretic analysis of the protein products of 42 loci. Strains with higher heterozygosities had faster development rates, as measured by hatching time, than strains with lower heterozygosity. Concordance between hatching time and another measure of development rate, degree of yolk-sac resorption, suggests that hatching time is a valid measure of embryonic development rate in salmonid fishes. Earlier-hatching embryos were longer and heavier at the time of yolk-sac resorption than later-hatching fish. Females from more-heterozygous strains also had a tendency to have larger eggs. These data suggest that genetic variation is an important biological resource to be conserved in hatchery stocks.     

Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), and its implications for reintroduction

The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.     

Electrophoretic variation in six populations of brown trout (Salmo trutta L.)

Starch gel electrophoretic studies of 16 enzymes encoded by 34 Loci were performed on six brown trout populations. One new polymorphism is described at the Pmi-2 locus. Breeding data were analysed for both single and joint segregation of six loci: Aat-1, Cpk-1, G3p-2, Mdh-2, Mdh-3, and Pmi-2. All the loci are shown to segregate in simple mendelian ratios and one nonrandom joint segregation was observed. The polymorphism level, heterozygosities, and genetic distances were estimated and compared with those reported in other studies on brown trout and closely related salmonid species. The polymorphism level (25%) and average heterozygosity (9%) were high. Significant genetic distances were observed, but the average degree of differentiation between populations appeared to be small (9% of the total heterozygosity).     

Analysis of Heterozygosity at the PI, TF, PGM1, ACP1, HP, GC, GLO1, C3, and ESDLoci in Pulmonary Tuberculosis Patients Differing in Response to Treatment

Heterozygosity at nine genetic loci (PI, TF, PGM1, ACP1, HP, GC, GLO1, C3, and ESD) was analyzed in pulmonary tuberculosis patients with good (group 1, N= 71) and poor (group 2, N= 35) response to treatment. The observed heterozygosities were compared with the expected values, which were calculated from allele frequencies in a control sample of healthy individuals (N= 328 with all but one locus and 78 with ESD) according to Hardy–Weinberg expectations. The analysis showed that the observed heterozygosities g _l of patients significantly differed from the expected values h _lin the case of four loci (GC, PI, C3, and ACP1). The observed heterozygosity was higher than expected in three cases (PI, C3, and ACP1) and lower then expected (GC) in one case. When data on each individual locus were compared using Fisher's exact test, both groups of patients proved to significantly differ (P _F< 0.05) from the control group in the same four loci. No difference in observed heterozygosity was detected between the two groups of patients. The mean expected heterozygosity was h¯= 0.386 ± 0.00674; the mean observed heterozygosity was g¯ = 0.415 ± 0.02 in group 1, g¯ = 0.402 ± 0.026 in group 2, and g¯ = 0.371 ± 0.00955 in the control group. The ttest did not reveal a significant difference between the mean values of expected observed heterozygosities. Heterozygosity at individual loci, rather than mean heterozygosity, was proposed as an integral nonspecific indicator of the genetic control of a disease, because the former directly implicates individual marker loci in the development of a disorder, whereas effects of individual loci may eliminate each other when mean heterozygosity is computed. Based on the results obtained, a genetic control was assumed for the development of the tuberculosis process in the lungs.     

猪F2设计资源家系中4条染色体微卫星标记分析

利用中国地方猪种蓝塘猪(16头母猪)与外来品种长白猪(8头公猪)按F2设计建立资源家系, 根据美国肉畜中心(USDA-MARC 2.0)公布的猪连锁图谱, 在1、4、7和8号染色体上间隔10~20 cM选择一个微卫星标记, 共31个标记, 采用WAVEÒ核苷酸片段分析系统和ABI 377 DNA序列分析仪检测资源群体的P、F1和F2代个体微卫星的基因型, 对其基因频率、杂合度和多态信息含量等进行统计分析。结果发现: 利用ABI 377检测的猪1、4和8号染色体上的有效微卫星标记21个, 其中13个标记的18个等位基因片段大小超过了网上已报道的结果, 发现新等位基因的标记占62%; 在31个微卫星标记中, 杂合度(h)在0.043~0.7855之间, 总平均杂合度为0.6460, 其中70%座位的h>0.60; 总平均多态信息含量(PIC)为0.5949, 有77.4%位点的PIC>0.5。统计分析结果表明, 选用的微卫星标记能够较好地提供标记信息, 为进一步在该家系中进行猪重要性状的QTL定位打下了良好的基础。     

Microgeographic population genetic structure in the northern water snake, Nerodia sipedon sipedon detected using microsatellite DNA loci

We describe the isolation and genetic characterization of eight microsatellite DNA loci from the northern water snake, Nerodia sipedon sipedon and use these loci to analyse levels of genetic differentiation between local (< 2 km apart) populations of these snakes in Ontario. These loci are variable, with expected heterozygosities ranging from 0.28 to 0.91, and can correctly exclude nonsires in parentage analyses with a high probability (0.998). Population analyses reveal significant deviation from expected heterozygosity levels for one population, probably a result of a null allele(s) at a single locus and small but significant levels of genetic differentiation among all three populations. This demonstrates that microgeographic genetic structure exists in this species, possibly due to limited dispersal.