EFFECTS OF POPULATION BOTTLENECKS ON GENETIC DIVERSITY AS MEASURED BY ALLOZYME ELECTROPHORESIS

Low levels of allozyme heterozygosity in populations are often attributed to previous population bottlenecks; however, few experiments have examined the relationship between heterozygosity and bottlenecks under natural conditions. The composition and number of founders of 55 experimental populations of the eastern mosquitofish (Gambusia holbrooki), maintained under simulated field conditions, were manipulated to examine the effects of bottlenecks on three components of allozyme diversity. Correlations between observed and expected values of allozyme heterozygosity, proportions of polymorphic loci, and numbers of alleles per locus were 0.423, 0.602, and 0.772, respectively. The numbers of polymorphic loci and of alleles per locus were more sensitive indicators of differences in genetic diversity between the pre-bottleneck and post-bottleneck populations than was multiple-locus heterozygosity. In many populations, single- and multiple-locus heterozygosity actually increased as a result of the founder event. The weak relationship between a population's heterozygosity and the number and composition of its founders resulted from an increase in the variance of heterozygosity due to drift of allele frequencies. There was little evidence that selection influenced the loss of allozyme variation. When it is not possible to estimate heterozygosity at a large number of polymorphic loci, allozyme surveys attempting to detect founder events and other types of bottlenecks should focus on levels of locus polymorphism and allelic diversity rather than on heterozygosity.     

Yield components of potato microtubers: in vitro production and field performance

Genetic parameters, character association and path analysis for yield components of microtuber production in vitro and their field performance were studied in 37 potato (Solanum tuberosum L.) genotypes. Among the microtuber yield components, average microtuber weight had maximum genotypic (or phenotypic) coefficient of variation, heritability and predicted genetic advance; however, the estimated values of these genetic parameters were maximum for tuber yield among the field yield components. The heritability estimates of field yield components were higher than that of their corresponding in vitro yield components of microtuber production. The highest correlation coefficients between average microtuber weight and microtuber yield suggested that microtuber weight was more important than microtuber number in determining microtuber yield potential in vitro. However, tuber number was found to be more important than tuber weight in determining tuber yield potential under field conditions. Average microtuber weight had maximum direct effect on microtuber yield, whereas tuber number had maximum direct effect on tuber yield under field conditions. The study showed that the relative importance of the components of microtuber production in vitro differed from that of corresponding field yield components. The expression of a genotype for microtuber production in vitro is different from that of tuber production under field situation i.e. the performance of a genotype in vitro is not a measure of its field performance.     

Relationship between heterozygosity and genetic distance in the three major races of man

In pairwise comparisons of gene frequency data from the three major races of man, the single locus measures of the heterozygosity within and the genetic distance between races are shown to be strongly correlated across the loci coding for red cell proteins and enzymes. The intercept of the regression line of genetic distance on heterozygosity in protein enzyme loci is statistically insignificant. These findings suggest that the genetic variability at the enzyme and protein loci in man is probably maintained by a balance of mutation and random genetic drift. At the blood group loci, however, the observed relationship between genetic distance and heterozygosity does not follow the expectation of the neutral mutation hypothesis. These observations are discussed in terms of the changes in probability of identical monomorphism in two populations during the process of gene differentiation.     

Allozyme frequencies, heterozygosity and genetic distances following S1 recurrent selection in two synthetic maize populations

 Three cycles of S₁ recurrent selection for yield were carried out in two synthetic maize populations, EPS6 from humid Spain and EPS7 from arid Spain. One-hundred S₁ lines were evaluated from each cycle of selection and the ten highest-yielding S₁ lines were recombined to produce the next cycle. Changes in variability and genetic distances in two synthetic maize populations, following three cycles of recurrent selection, recombining ten S₁ lines in each cycle, were determined. Isozyme analysis was performed on 125 seedlings per cycle of selection (four cycles in each of two populations). Regressions of each allozyme frequency on cycles of selection were performed, genetic distances between populations were determined, and simple correlations between genetic distances and heterosis were calculated. The average heterozygosity per locus was also calculated for each population. Regression analysis did not reveal any common trend between EPS6 and EPS7 for changes in allele frequencies presumably due to selection. The number of polymorphic loci, the mean alleles per locus, and the mean heterozygosity did not show any reduction in variability. Finally, selection did not affect genetic distances among cycles of selection. The agronomic evaluation of the selection program, after three cycles of selection, revealed that the genetic variance was not significantly reduced for most traits, and that the heterosis among cycles of selection of both populations had not changed significantly. The conclusions based on isozyme data supported the deductions made from agronomic data. Three cycles of selection neither caused relevant changes on variability nor on genetic distance among cycles of selection of both maize synthetic populations. These data did not indicate any basis for increasing the number of S₁ lines recombined for recurrent selection. Received: 28 April 1997 / Accepted: 23 June 1997     

Use of molecular markers in participatory plant breeding: assessing the genetic variability in cotton populations bred by farmers

In participatory plant breeding, farmers are involved in simple selection schemes that are not suitable for assessing genetic variability in the segregating populations. We propose to use information derived from molecular marker analyses to help monitoring such populations. In this study, we used three indicators to compare genetic variability in eight genetic structures, that is three plant populations selected by farmers over five generations, three nonselected populations and two commercial varieties. The three indicators were the polymorphic locus rate, heterozygosity rate and dissimilarity index. The results highlighted that the genetic variability decreased more with farmers’ selection than with environmental factors. The breeding process was not complete because genetic variability in the selected populations was midway between that of the nonselected populations and that of the commercial varieties monitored. The three proposed indicators were relevant for describing the studied populations. They could be interpreted according to a grid drawn up on the basis of the results of the present study.     

Heterozygosity at a single locus explains a large proportion of variation in two fitness‐related traits in great tits: a general or a local effect?

In natural populations, mating between relatives can have important fitness consequences due to the negative effects of reduced heterozygosity. Parental level of inbreeding or heterozygosity has been also found to influence the performance of offspring, via direct and indirect parental effects that are independent of the progeny own level of genetic diversity. In this study, we first analysed the effects of parental heterozygosity and relatedness (i.e. an estimate of offspring genetic diversity) on four traits related to offspring viability in great tits (Parus major) using 15 microsatellite markers. Second, we tested whether significant heterozygosity–fitness correlations (HFCs) were due to ‘local’ (i.e. linkage to genes influencing fitness) and/or ‘general’ (genome‐wide heterozygosity) effects. We found a significant negative relationship between parental genetic relatedness and hatching success, and maternal heterozygosity was positively associated with offspring body size. The characteristics of the studied populations (recent admixture, polygynous matings) together with the fact that we found evidence for identity disequilibrium across our set of neutral markers suggest that HFCs may have resulted from genome‐wide inbreeding depression. However, one locus (Ase18) had disproportionately large effects on the observed HFCs: heterozygosity at this locus had significant positive effects on hatching success and offspring size. It suggests that this marker may lie near to a functional locus under selection (i.e. a local effect) or, alternatively, heterozygosity at this locus might be correlated to heterozygosity across the genome due to the extensive ID found in our populations (i.e. a general effect). Collectively, our results lend support to both the general and local effect hypotheses and reinforce the view that HFCs lie on a continuum from inbreeding depression to those strictly due to linkage between marker loci and genes under selection.     

High genetic variability in an ecologically variable vertebrate,Bufo viridis

Allozymic variation in proteins encoded by 26 loci was analyzed electrophoretically in 517 specimens of green toads from 11 populations from Israel and one population from Vis Island in the Adriatic Sea. Genetic variation in this toad is the highest yet reported in any vertebrate. All three genetic parameters, mean number of alleles per locus (A), mean proportion of loci polymorphic per population (P), and mean number of heterozygous loci per individual (H), are very high (A = 1.65, range 1.38-2.04; P = 0.423, range 0.346-0.615; H = 0.133, range 0.108-0.159). Central and marginal mainland populations are only slightly more variable than desert isolates, but much more variable than the Vis Island population. Genetic similarity is very high between mainland populations (S = 0.951, range 0.93-0.97). Frequencies of two alleles (Icd-lc and Tfa) are correlated with an ecological gradient of increasing aridity. Regulatory enzymes appeared to contribute more to overall polymorphism than non-regulatory enzymes. The genetic variation observed suggests that selection for heterozygosity as an adaptive strategy is operating in the ecologically variable environment in which green toads live.     

Psorophora columbiae and Psorophora toltecum (Diptera: Culicidae) Colombian populations cannot be differentiated by isoenzymes

Two populations of the mosquito Psorophora columbiae from the central Andean area of Colombia and one population of Ps. toltecum from the Atlantic coast of Colombia were analyzed for 11 isoenzyme markers. Psorophora columbiae and Ps. toltecum are two of the main vectors of Venezuelan equine encephalitis. We found no conspicuous genetic differences between the two species. The relatively high gene flow levels among these populations indicate that these are not two different species or that there has been recent divergence between these taxa. In addition, no global differential selection among the loci was detected, although the alpha-GDH locus showed significantly less genetic heterogeneity than the remaining loci, which could mean that homogenizing natural selection acts at this locus. No isolation by distance was detected among the populations, and a spatial population analysis showed opposite spatial trends among the 31 alleles analyzed. Multiregression analyses showed that both expected heterozygosity and the average number of alleles per locus were totally determined by three variables: altitude, temperature and size of the human population at the locality. Individually, the expected heterozygosity is more related to these three variables than to the average number of alleles.     

Allopolyploidy in the Thalloid Liverwort Corsinia (Marchantiales)

The thalloid liverwort Corsinia coriandrina includes morphologically similar haploid and polyploid populations with an allopatric geographical distribution. Haploid and polyploid colonies of the Old World, and one polyploid colony from Texas have been analysed. The polyploid, monoecious cytotype has a wider geographical range and ecological tolerance than the haploid, dioecious cytotype which appears to be restricted to southern Europe and Macaronesia. Similarity coefficients between the two Old World cytotypes based on isozyme data show them to be more genetically divergent than suggested by their morphology, and to fit the definition of sibling species. Fixed heterozygosity in six of eight enzyme loci suggests an alloploid origin of the Old World polyploids. The haploid cytotype could be one of the putative parents. Alleles in the polyploid that were not detected in the haploid are presumably derived from an unknown progenitor. The polyploid New World colony shows significant genetic divergence; it represents a different allopolyploid sibling species. Accordingly, at least two independent origins of the polyploid must be supposed; one in the Old World; the other in the New World. The presumed autopolyploid origin of polyploid liverworts is once more challenged by our analysis of polyploid Corsinia. Indeed, autopolyploidy has still not been documented conclusively in any polyploid liverwort.     

Sampling Variances of Heterozygosity and Genetic Distance

Mathematical formulae for the sampling variances of average heterozygosity and Nei's genetic distance are developed. These sampling variances are decomposed into their two components, i.e. the inter-locus and intra-locus variances. The relationship between the number of loci and the number of individuals per locus to be examined for estimating average heterozygosity and genetic distance is also discussed. The utility of the inter-locus variance of heterozygosity for studying the mechanism of maintenance of genetic variability in populations is indicated.     

Exploring the relationship between parental relatedness and male reproductive success in the Antarctic fur seal Arctocephalus gazella

Recent genetic studies of natural populations have shown that heterozygosity and other genetic estimates of parental relatedness correlate with a wide variety of fitness traits, from juvenile survival and parasite resistance to male reproductive success. Many of these traits involve health and survival, where the underlying mechanism may involve changes in the effectiveness of the immune system. However, for traits such as reproductive success, the likely mechanisms remain less obvious. In this paper, we examine the relationship between heterozygosity and a range of traits that contribute to male reproductive success, including time spent on territories and competitiveness. Our analysis is based on observational and genetic data from eight consecutive breeding seasons at a colony of the Antarctic fur seal, Arctocephalus gazella. Overall, male reproductive success was found to correlate strongly with internal relatedness (IR, a form of heterozygosity). When different components of success were analyzed, we found that IR correlates independently with reproductive longevity, time spent ashore, and competitive ability per unit mating opportunity on the study beach, with more heterozygous males being more successful. Behavioral observations were sufficiently detailed to allow examination of how daily mean IR values for males present on the beach varied within seasons and from year to year. Again, significant variation was found both among and within seasons, with more homozygous males appearing less able to hold territories in poor seasons when pup production is low and, within a season, at both the start of the season and to some extent around the peak of female estrus. Finally, we tested whether the benefits of high heterozygosity are due mainly to a genomewide effect (e.g. inbreeding depression) or to single locus heterosis by asking whether the relationship between IR and male success was robust to the removal of any single locus or to any pair of loci. Since the relationship remained significant in all cases, we favor a multilocus explanation for the effects we report.     

Genetic diversity and parentage assignment in Dojo loach,Misgurnus anguillicaudatus based on microsatellite markers

In this study, genetic diversity and structure of three Misgurnus anguillicaudatus populations from three different geographical locations in China (Hunan, Hubei and Henan province) were investigated using microsatellite markers. High level of genetic diversity of all three populations was revealed by expected heterozygosity (H_e), observed heterozygosity (H_o) and allele number. Significant genetic differentiations were found between all pairs of populations. The efficiency of eight microsatellite markers in parentage assignment of 540 progeny from twenty full-sib families was evaluated. Simulation based on allele frequency data demonstrated that probabilities of exclusion per locus range from 0.313 to 0.825 when no parent information is available and 0.504 to 0.904 when one parent is known. The assignment success rate based on the real data using eight markers was 96.85%. This study indicates that these M. anguillicaudatus resources are valuable genetic and breeding material for aquaculture and the microsatellite markers will be useful for investigation of genetic background and molecular marker-assisted selective breeding in this species.     

A GENETIC PERSPECTIVE OF MAMMALIAN VARIATION AND EVOLUTION IN THE INDONESIAN ARCHIPELAGO: BIOGEOGRAPHIC CORRELATES IN THE FRUIT BAT GENUS CYNOPTERUS

This study investigated allozyme and morphometric variability within the genus Cynopterus, with particular emphasis on C. nusatenggara, which is endemic to Wallacea, the area encompassing the Oriental-Australian biogeographic interface. The genetic distances between Cynopterus species are small by mammalian standards and suggest that this genus has undergone a recent series of speciation events. The genetic distance between populations of C. nusatenggara is strongly correlated with both the contemporary sea-crossing distance between islands and the estimated sea crossing at the time of the last Pleistocene glacial maximum, 18,000 b .p . This observation, together with low levels of population substructure within islands as shown by F-statistics, indicates that the sea is a primary and formidable barrier to gene exchange. The genetic distance and the great-circle geographical distance between the populations of C. nusatenggara are not correlated, although a principal-coordinates analysis of genetic distance reveals relationships between the populations that are similar to their geographical arrangement. A strong negative correlation exists between the level of heterozygosity within island populations of C. nusatenggara and the minimum sea-crossing distance to the nearest large source population. This is interpreted as reflecting an isolation effect of the sea, leading to reduced heterozygosity in populations that have larger sea barriers between them and the large source islands. Independently of this, heterozygosity is negatively associated with longitude, which in turn is associated with systematic changes in the environment such as a gradual decline in rainfall from west to east. The association between heterozygosity and longitude is interpreted as reflecting an association between genetic and environmental variance and supports the niche-width theory of genetic variance. Morphometric variability did not show any of the main effects demonstrated in the genetic data. Furthermore, there was no evidence that, at the level of individuals, genetic and morphometric variability were associated.     

三个虹鳟养殖群体遗传结构的微卫星分析

利用20个微卫星标记对3个虹鳟(Oncorhynchus mykiss)养殖群体进行遗传结构分析。结果表明,(1)3个群体检测的平均等位基因数为3·6～4·1,平均观测杂合度为0·5224～0·6328,平均期望杂合度为0·4736～0·5522,平均多态信息含量为0·4354～0·5084,说明这几个群体多态性属于偏高水平,遗传多样性高。通过d值,确定了Hard-Weinberg平衡的偏离情况,发现AY039638、AY039646在3个群体中都表现为不平衡。对3个群体的遗传距离进行了估算,并进行聚类分析,本溪的两个群体先聚为一支,再与渤海群体相聚,显示出明显的地理特征。(2)本溪虹鳟群体在位点AF352770出现部分等位基因消失的现象;AF352754在本溪群体中表现为位点消失,可作为区分本溪群体和渤海群体的分子标记。(3)综合评价3个群体,渤海站虹鳟群体的遗传多样性最高,与前人研究结果一致。     

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.     

Fluctuating asymmetry and genetic variability in the roe deer (Capreolus capreolus): a test of the developmental stability hypothesis in mammals using neutral molecular markers

Fluctuating asymmetry (FA), used as an indicator of developmental stability, has long been hypothesized to be negatively correlated with genetic variability as a consequence of more variable organisms being better suited to buffer developmental pathways against environmental stress. However, it is still a matter of debate if this is due to metabolic properties of enzymes encoded by certain key loci or rather to overall genomic heterozygosity. Previous analyses suggest that there might be a general difference between homeo- and poikilotherms in that only the latter tend to exhibit the negative correlation predicted by theory. In the present study, we addressed these questions by analysing roe deer (Capreolus capreolus) from five German populations with regard to FA in metric and non-metric skull and mandible traits as well as variability at eight microsatellite loci. Genetic variability was quantified by heterozygosity and mean d2 parameters, and although the latter did not show any relationship with FA, we found for the first time a statistically significant negative correlation of microsatellite heterozygosity and non-metric FA among populations. Because microsatellites are non-coding markers, this may be interpreted as evidence for the role of overall genomic heterozygosity in determining developmental stability. To test if the threshold character of non-metric traits is responsible for the metric vs non-metric difference we also carried out calculations where we treated our metric traits as threshold values. This, however, did not yield significant correlations between FA and genetic variability either.     

Offspring fitness in relation to population size and genetic variation in the rare perennial plant species Gentiana pneumonanthe (Gentianaceae)

Seeds were sampled from 19 populations of the rare Gentiana pneumonanthe, ranging in size from 5 to more than 50,000 flowering plants. An analysis was made of variation in a number of life-history characters in relation to population size and offspring heterozygosity (based on seven polymorphic isozyme loci). Life-his-tory characters included seed weight, germination rate, proportion of seeds germinating, seedling mortality, seedling weight, adult weight, flower production per plant and proportion of plants flowering per family. Principal component analysis (PCA) reduced the dataset to three main fitness components. The first component was highly correlated with adult weight and flowering performance, the second with germination performance and the third component with seed and seedling weight and seedling mortality. The latter two components were considered as being maternally influenced, since these comprised life-history traits that were significantly correlated with seed weight. Multiple regression analysis showed that variation in the first fitness component was mainly associated with heterozygosity and not with population size, while the third fitness component was only correlated with population size and not with heterozygosity. The latter relationship appeared to be non-linear, which suggests a stronger loss of fitness in the smallest populations. The second (germination) component was neither correlated with population size nor with genetic variation. There was only a weak association between population size, heterozygosity and the population coefficients of variation for each life history character. Most correlation coefficients were negative, however, which suggests that there is more variation among progeny from smaller populations. We conclude that progeny from small populations of Gentiana pneumonanthe show reduced fitness and may be phenotypically more variable. One of the possible causes of the loss of fitness is a combination of unfavourable environmental circumstances for maternal plants in small populations and increased inbreeding. The higher phenotypic variation in small populations may also be a result of inbreeding, which can lead to deviation of individuals from the average phenotype through a loss of developmental stability.     

Patterns of genetic variability at individual minisatellite loci in minke whale Balaenoptera acutorostrata populations from three different oceans

The genetic variability at six cloned minisatellite loci was analyzed in minke whale populations from the North Atlantic, North Pacific, and Antarctic Oceans. Three loci displayed only a few different alleles in each of the three populations, with heterozygosity ranging from 0.00 to 0.47, and three loci revealed many different alleles in at least two fo the three populations, with heterozygosity ranging up to 0.98. Using small sample sizes, samples from two adjacent Antarctic Management Areas were not found to differ significantly in allele frequencies at any of the six loci. The use of principal coordinate analysis to detect multilocus disequilibria was explored. No significant evidence was found of intrapopulation heterogeneity within the pooled Antarctic sample. Pronounced interoceanic differences were observed at every locus, confirming the existence of genetic isolation found earlier using more conventional marker systems. The populations from the three oceans appear to have diverged to such a degree that the hypervariable loci have had time to evolve independently and arrive at different evolutionary stages in different populations. The frequency of undetected "null" alleles is remarkably high in minke whale populations compared to human populations and is probably a result of the cloning protocol used. Minisatellite loci are shown to provide a powerful population genetic tool, supplying levels of resolution appropriate to different degrees of evolutionary divergence.      

Isolation and characterization of 15 nuclear microsatellite markers for Baillonella toxisperma Pierre (Sapotaceae), a low-density tree species of Central Africa

Baillonella toxisperma is a scattered endemic species of the Guineo-Congolian forest. We developed 15 nuclear microsatellite markers specifically for B. toxisperma to analyse the genetic diversity of 188 individuals distributed in two natural populations in Gabon. On average, 8.3 alleles per locus were identified; observed heterozygosity ranged from 0.056 to 0.872 and expected heterozygosity from 0.282 to 0.823 among populations. Only three loci showed a significant departure to Hardy-Weinberg equilibrium, but no linkage disequilibrium was observed for any pair of loci.     

Allozyme variation in populations, full-sib families and selfed lines in Betula pendula Roth

Changes in genetic variability in populations (stand origins), full-sib (FS) families and three generations of selfed lines of Betula pendula were observed based on 15 allozyme loci. Growth vigour, measured as stem volume, and its relationship with heterozygosity was studied to determine the effect of inbreeding. Pooled FS families showed a higher percentage of polymorphic loci (P) and allelic numbers per locus (A) than those of natural populations, but no difference in heterozygosity. There was no difference in allozyme variability between fast-and slow-growing family groups, and heterozygosity was not correlated with stem volume among FS families. Allozyme variability was significantly decreased in advancing generations of selfing, and the further the selfing generation, the lower the heterozygosity and the slower the growth. Observed heterozygosity after advancing generations of inbreeding was increasingly higher than expected, indicating overdominance effects or, alternatively, selection against deleterious homozygotes.