Estimation of heterozygosity for single-probe multilocus DNA fingerprints

In spite of the increasing application of DNA fingerprinting to natural populations and to the genetic identification of humans, explicit methods for estimation of basic population genetic parameters from DNA fingerprinting data have not been developed. Contributing to this omission is the inability to determine, for multilocus fingerprinting probes, relatively important genetic information, such as the number of loci, the number of alleles, and the distribution of these alleles into specific loci. One of the most useful genetic parameters that could be derived from such data would be the average heterozygosity, which has traditionally been employed to measure the level of genetic variation within populations and to compare genetic variation among different loci. We derive here explicit formulas for both the estimation of average heterozygosity at multiple hypervariable loci and a maximum value for this estimate. These estimates are based upon the DNA restriction-pattern matrices that are typical for fingerprinting studies of humans and natural populations. For several empirical data sets from our laboratory, estimates of average and maximal heterozygosity are shown to be relatively close to each other. Furthermore, variances of these statistics based on simulation studies are relatively small. These observations, as well as consideration of the effect of missing alleles and alternate numbers of loci, suggest that the average heterozygosity can be accurately estimated using phenotypic DNA fingerprint patterns, because this parameter is relatively insensitive to the lack of certain genetic information.      

Compensatory Aspects of Allele Diversity at Immunoglobulin Loci: Gene Correlations in Rabbit Populations Devoid of Light Chain Diversity (Oryctolagus Cuniculus L.; Kerguelen Islands)

Is there a selective advantage of increased diversity at one immunoglobulin locus when diversity at another locus is low? A previous paper demonstrated excess heterozygosity at the rabbit light chain b locus when heterozygosity was low at the heavy chain constant region e locus. Here we consider the reverse situation by analyzing allele distributions at heavy chain loci in populations fixed for the light chain b locus. We analyzed the a locus that encodes the predominantly expressed heavy chain variable region, and the d and e loci that control different parts of the Ig gamma class constant region. While there was excess heterozygosity, genetic differentiation between localities was extensive and was most pronounced for females. This was in marked contrast with observations in areas where b-locus diversity was important and confirms a negative correlation between e- and b-locus heterozygosity. Trigenic disequilibria corresponded to a significant negative correlation between e- and a-locus heterozygosity due mainly to strong variation among localities within the context of pronounced (digenic) linkage disequilibria. Although substantial, the average increase in a/e-locus single heterozygosity implemented by higher order disequilibria within localities was not significant.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. II. Estimates of Heterozygosity and Patterns of Geographic Differentiation

A study of genic variation in natural population of D. melanogaster was undertaken (1) to obtain a better estimate of heterozygosity by sampling a relatively large number of gene loci and (2) to identify different groups of polymorphic loci whose variation patterns might suggest different kinds of selection forces. A total of 117 gene loci (coding for 79 enzymes and 38 abundant proteins) were studied in 15 geographically distant populations originating from different continents. The findings of this study are as follows: (1) of the 117 gene loci studied, 61 are polymorphic and 56 are uniformly monomorphic everywhere. (2) An average population is polymorphic for 43% of its gene loci and an average individual is heterozygous for 10% of its gene loci. These estimates are remarkably similar among populations. (3) The average within-locality heterozygosity (H(S)) for polymorphic loci is uniformly distributed over the range of heterozygosity observed; i.e. , given that a locus has any local variation, it is nearly as likely to have a lot as a little. (4) The distribution of F(ST) (fixation index) is strongly skewed, with a prominent mode at 8-10% and a long tail of high values reaching a maximum of 58%. Two-thirds of all loci fall within the bell-shaped distribution centered on an F(ST) of 8-10%, a result compatible with the notion that they are experiencing a common tendency toward small interlocality differences owing to extensive gene flow among populations. (5) The distribution of total heterozygosity (H(T)) has a prominent bimodal distribution. The lower mode consists of loci with single prominent allele and a few uncommon ones and the upper mode consists of clinally varying loci with a high F(ST ) (e.g., Adh and G6-pd), loci with many alleles in high frequency (e.g., Ao and Xdh) and loci with two alleles in high frequency in all populations but, with little interpopulational differentiation (e.g., Est-6 and alpha-Fuc). The loci in the lower mode are probably under purifying selection; a large proportion of those in the latter mode may be under balancing selection. (6) Comparison of genic variation for loci located inside vs. outside inversions, comparison of F(ST) for inversions and their associated genes, and comparison of F(ST) and map position for pairs of loci all suggest that, while linkage has some influence, it does not seem to constrain the pattern of variation that a locus may develop. (7) Eighteen polymorphic loci show latitudinal variation in allele frequencies which are consistent in populations from different continents. (8) Estimates of Nei genetic distance between population pairs are generally low between populations on the same continent and high between populations on different continents. There are two important exceptions: population pairs for which both localities are in the temperate zone show no relationship to distance, and in cases where both populations are tropical or subtropical, the genetic distance is higher than for the temperate-tropical comparisons and seem even higher than one would expect from the geographic distance separating them. The latter observation suggests that either geographic separation outweighs differences in environment in determining the genetic composition of a population or that all tropical populations are not experiencing the same environment.-The results are discussed in relation to the neutralist-selectionist controversy of genic variation and two important conclusions are drawn: First, there is a negative correlation between the number of loci sampled and the resulting heterozygosity. This means that available estimates of heterozygosity, 85% of which are based on 30 or fewer loci, are high and hence not appropriate for making between-taxa comparisons. Secondly, there is a group of loci, comprising one-third of polymorphic loci (or about 15% of all loci studied), that is distinguishable by different patterns of variation within and among populations. Most of these loci have clinal variation which is consistent with the hypothesis that their genetic variation is maintained by balancing selection.     

Genetical variation in three Pacific House mouse (Mus musculus) populations

Studies of allozymic variation at 36 loci in samples of House mouse ( Mus musculus ) populations collected from the island of Hawaii and two islets in the Enewetak Atoll, Marshall Islands are reported. All three populations carried a great deal of inherited variation: the Hawaiian sample had a mean heterozygosity of 16.6% per locus, which is the highest value so far found for a mouse population. The mean heterozygosities for the two atoll populations were 11.4% and 10.9%.
There were no changes in either heterozygosity or allozyme frequencies with age. In this respect, these populations from the tropical Pacific differed from populations living in cold temperate regions where natural selection has been shown to affect allele frequencies in different ways at different stages of the life cycle.     

Signatures of demographic history and natural selection in the human major histocompatibility complex Loci

Many lines of evidence show that several HLA loci have experienced balancing selection. However, distinguishing among demographic and selective explanations for patterns of variation observed with HLA genes remains a challenge. In this study we address this issue using data from a diverse set of human populations at six classical HLA loci and, employing a comparative genomics approach, contrast results for HLA loci to those for non-HLA markers. Using a variety of analytic methods, we confirm and extend evidence for selection acting on several HLA loci. We find that allele frequency distributions for four of the six HLA loci deviate from neutral expectations and show that this is unlikely to be explained solely by demographic factors. Other features of HLA variation are explained in part by demographic history, including decreased heterozygosity and increased LD for populations at greater distances from Africa and a similar apportionment of genetic variation for HLA loci compared to putatively neutral non-HLA loci. On the basis of contrasts among different HLA loci and between HLA and non-HLA loci, we conclude that HLA loci bear detectable signatures of both natural selection and demographic history.     

Allozyme and chromosomal polymorphism ofDrosophila buzzatii in Brazil and Argentina

Allozyme polymorphism in the colonizing populations ofD. buzzatii in Australia is quite low (average heterozygosity of 0.051 ± 0.025), but no comparative data are available for the species in other introduced populations or in its presumed area of origin, the Chaco of Argentina. For 12 localities in Argentina and five in Brazil, average expected heterozygosity is not significantly different from that in Australia. However, there appears to have been a loss of genetic variability on introduction of the species to Australia, as five loci are variable in South America that are monomorphic in Australia, and one additional allele was detected at each of six other loci in South America. Our results for inversion polymorphism in Argentina are consistent with previous data, but some Brazilian populations apparently have reduced inversion polymorphism. With the exception of those nearest the Chaco, these Brazilian populations may have resulted from passive colonization within historical times due to transport by man, and could represent both primary and secondary colonizations. However, the allozyme data do not readily fit a colonization hypothesis, and theD. buzzatii populations of both northeast and southeast Brazil may be relic populations. More detailed study of inversion and allozyme polymorphism in Brazil is necessary to provide critical data on the evolutionary history of this species.     

Genetic variation and population subdivision in the cricket frog Acris crepitans

Genetic variation at 16 enzyme loci was examined for Acris crepitans, from 14 populations collected along an intermittent creek in north-central Texas and seven populations from separate localities in south-central Texas. Regional genetic differentiation was low. Zygotic distributions for the 14 creek populations were significantly heterogeneous, and genic heterogeneity (F_ST=0.116) was nearly as high as that for widely separated populations (F_ST=0.136). There was no relationship between genetic similarity and proximity of the populations. Gene flow between adjacent populations is minimal, and differentiation appeared to be maintained by a combination of stochastic events and inbreeding.     

Genetic Heterogeneity within Electrophoretic "Alleles" of Xanthine Dehydrogenase in DROSOPHILA PSEUDOOBSCURA

An experimental plan for an exhaustive determination of genic variation at structural gene loci is presented. In the initial steps of this program, 146 isochromosomal lines from 12 geographic populations of D. pseudoobscura were examined for allelic variation of xanthine dehydrogenase by the serial use of 4 different electrophoretic conditions and a head stability test. The 5 criteria revealed a total of 37 allelic classes out of the 146 genomes examined where only 6 had been previously revealed by the usual method of gel electrophoresis. This immense increase in genic variation also showed previously unsuspected population differences between the main part of the species distribution and the isolated population of Bogotá population. The average heterozygosity at the Xdh locus is at least 72% in natural populations. This result, together with the very large number of alleles segregating and the pattern of allelic frequencies, has implications for theories of genetic polymorphism which are discussed.     

Comparison of gene flow estimates between species of darters in different streams

Allozyme variation was assessed at two localities for 38 loci in Etheostoma blennioides and 43 loci in E. flabellare . Percent polymorphism (P) ranged from 18·4 to 31·6 and average heterozygosity (H) ranged from 0·026 to 0·079. Estimates of gene flow indicated panmictic populations of E. blennioides and sub-divided populations of E. flabellare , with significantly more substructuring of E. flabellare from one population. Population structuring of E. flabellare and no structuring of E. blennioides is consistent with predictions based on life history data. Significantly different gene flow estimates for E. flabellare between streams imply that each stream environment induced different population structures. Reduced heterozygosity for both species and significantly less population structuring in one population are consistent with drought-induced extinction and recolonization that probably occurs in the smaller stream.     

Genetic structure of natural populations of the red-spotted newt,Notophthalmus viridescens

Genetic variation is described at 15 loci in 2 neotenic and 12 nonneotenic populations of red-spotted newts. Though high levels of genetic similarity (I=0.990) were found among all populations, allele frequencies at six of the eight most polymorphic loci show significant heterogeneity across populations. Change in allele frequencies at two of these loci (Pep-2 and Ldh-1) is significantly correlated with latitude. Interspecific homologies are established for newt peptidases based on substrate specificities and lactate dehydrogenases based on tissue distribution, thermal stability, and kinetic properties. Nonneotenic populations are highly variable (H=0.157) and neotenic populations are only slightly, but significantly, less variable (H=0.120). The high levels of heterozygosity detected in nonneotenic populations may result from large effective population size and/or environmental heterogeneity. The unexpectedly high heterozygosity values obtained for the neotenic populations may indicate adult dispersal or the presence of some previously undetected red efts at these localities. In any case, a major change in life history has apparently had little effect on the genetic structure of these populations.This research was supported by grants from the Blakeslee Fund of Smith College.     

The variance of sample heterozygosity

The variance of sample heterozygosity, averaged over several loci, is studied in a variety of situations. The variance depends on the sampling implicit in the mating system as well as on that explicit in the loci scored and individuals sampled. There are also effects of allelic distributions over loci and of linkage or linkage disequilibrium between pairs of loci. Results are obtained for populations in drift and mutation balance, for infinite populations undergoing mixed self and random mating, and for finite monoecious populations with or without selfing. For unlinked loci in drift/mutation balance, variances appear to be lessened more by increasing the number of loci scored than by increasing the number of individuals sampled. For infinite populations under the mixed self and random mating system, however, the reverse is true. Methods for estimating the variance of sample heterozygosity are discussed, with attention being paid to unbalanced data where not all loci are scored in all individuals.     

Comparative studies of senescence in natural populations of guppies

Investigators have rarely sought evidence for senescence in natural populations because it is assumed that relatively few individuals will survive long enough in the wild to exhibit the intrinsic increase in mortality with age expected from senescent individuals. Nevertheless, senescence has been documented in some natural populations, mostly in birds and mammals. Here we report on a comparative study of senescence in two natural populations of guppies (Poecilia reticulata). We document senescence as an age-specific increase in mortality rate, with use of mark-recapture studies and implementation of program MARK for analysis of such observations. Extrinsic mortality was controlled for by choosing populations that experience low rates of predation because they coexist with only a single piscine predator (Rivulus hartii). These populations differ in their evolutionary history because one was native to such a site whereas the other was introduced to a site that previously contained no guppies. The source of the introduced guppies was a high-predation population downstream below a barrier waterfall. Theory predicts that the guppies derived from a high-predation locality should experience senescence at an earlier age than the native low-predation population; however, the historical differences among these populations are also confounded with everything else that differs among the two localities. We found that females from a natural low-predation population have delayed senescence compared with the recently established population and hence that the differences among localities in senescence conform to theoretical predictions. The males from natural low-predation environments also had lower overall mortality rates, but contrary to predictions, the pattern of senescence for males did not differ between populations. The difference between the sexes is potentially attributable to two factors that lower the statistical power for distinguishing differences in the age-specific acceleration of mortality in males. One factor is that males have higher mortality rates, so fewer survive to advanced ages. A second is that we had a greater ability to discriminate among older age classes in females. We also found that the introduced population sustained a higher rate of disease than the native low-predation population. Such disease may represent a confounding factor in our comparison, but it may also reflect one of the trade-offs inherent in the life-history differences of these populations.     

栖息条件对中华蜜蜂遗传多样性的影响

为了评估不同栖息条件对中华蜜蜂(简称中蜂)种群遗传多样性的影响,本研究运用微卫星标记的方法,对皖南山区4个不同采样点120个中华蜜蜂群体的2400只工蜂样本进行了分析.结果表明:与天然林野生中蜂群相比,单一茶树种植结构下,皖南中蜂群的等位基因数、平均期望杂合度和多态信息含量的差异均不显著;人工驯养中蜂群的等位基因数、多态信息含量差异显著,平均期望杂合度差异不显著;2006年采集的野生中蜂群与天然林野生中蜂群的等位基因数、平均期望杂合度和多态信息含量均差异显著.各种群间存在极显著的遗传分化,平均分化系数为0.32.说明皖南地区茶树单一化种植不会影响中蜂的遗传结构与资源保护.     

Temporal aspects of the fine-scale genetic structure in a population of Cinnamomum insularimontanum (Lauraceae)

Cinnamomum insularimontanum Hayata (Lauraceae) is an insect-pollinated, broad-leaved evergreen tree with bird-dispersed seeds. We used allozyme loci, Wright's fixation index, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among four age-classes within a recently founded study population (60 x 100 m area) in southern Korea. There were no significant differences in expected heterozygosity among age classes. However, significant genetic differentiation among age classes was detected (P<0.0001). Fixation indices within age classes showed significant deficits of observed heterozygosity, which may be caused by partial selfing. The homogeneity of genetic structure among four age-classes may reflect similar spatial patterns of seed immigration from surrounding populations occurring year after year. Finally, the average Moran's I and coancestry estimates indicated essentially random spatial distributions of alleles for each of the four age-classes and between seedlings and 2-4 year juveniles vs adult trees. These findings are very similar to those observed in the same study area for another member of the Lauraceae, Neolitsea sericea, which has a very similar life history and ecological characteristics (ie, bird-dispersed fruits, insect pollination, and a similar age structure). Together, these results suggest that the fleshy drupes of lauraceous species represent an adaptation to aid in the independent dispersal of seed by birds, which in turn may increase the genetic diversity of founders colonizing new habitats.     

Genetic polymorphism in the bladder campion,Silene maritima

A survey of protein variability has been made in wild populations of Silene maritima, a perennial outcrossing coastal plant. In the most extensively studied populations, at Beesands, six out of 21 loci were polymorphic, and the average heterozygosity was 0.153. Four polymorphic loci were studied on an extensive shingle beach at Dungeness. Three loci showed no frequency cline with distance from the sea; a fourth locus, that for adenylate kinase, showed a barely significant cline, which was not confirmed by a repeat study in the same place a year later. Five polymorphic loci were studied at Beesands along a strip of shingle beach and up a contiguous cliff. No frequency difference between the two habitats was observed. There are significant differences in allelic frequencies between localities. It is concluded that the data fail to show an association between habitat and gene frequency, although they were collected in such a way as to be capable of demonstrating such an association if it existed.     

LIFE-HISTORY EVOLUTION IN GUPPIES (POECILIA RETICULATA) 6. DIFFERENTIAL MORTALITY AS A MECHANISM FOR NATURAL SELECTION

We have previously reported a correlation between the life-history patterns of guppies and the types of predators with which they coexist. Guppies from localities with an abundance of large predators (high predation localities) mature at an earlier age and devote more resources to reproduction than those found in localities with only a single, small species of predator (low predation localities). We also found that when guppies were introduced from a high to low predation locality, the guppy life history evolved to resemble what was normally found in this low predation locality. The presumed mechanism of natural selection is differences among localities in age/size-specific mortality (the age/size-specific mortality hypothesis); in high predation localities we assumed that guppies experienced high adult mortality rates while in the low predation localities we assumed that guppies experienced high juvenile mortality rates. These assumptions were based on stomach content analyses of wild-caught predators and on laboratory experiments. Here, we evaluate these assumptions by directly estimating the mortality rates of guppies in natural populations. We found that guppies from high predation localities experience significantly higher mortality rates than their counterparts from low predation localities, but that these higher mortality rates are uniformly distributed across all size classes, rather than being concentrated in the larger size classes. This result appears to contradict the predictions of the age/size-specific predation hypothesis. However, we argue, using additional data on growth rates and the probabilities of survival to maturity in each type of locality, that the age-specific mortality hypothesis remains plausible. This is because the probability of survival to first reproduction is very similar in each type of locality, but the guppies from high predation localities have a much lower probability of survival per unit time after maturity. We also argue for the plausibility of two other mechanisms of natural selection. These results thus reveal mortality patterns that provide a potential cause of natural selection, but expand, rather than narrow, the number of possible mechanisms responsible for life-history evolution in guppies.     

Hybrid zone structure and the potential role of selection in hybridizing populations of native westslope cutthroat trout (Oncorhynchus clarki lewisi) and introduced rainbow trout (O. mykiss)

Introgressive hybridization is a common feature of many zones of contact between divergent lineages of fishes. This is particularly common when taxa that are normally allopatric come into artificial (human-induced) secondary contact. We examined 18 native populations of westslope cutthroat trout (Oncorhynchus clarki lewisi, WCT) to determine the extent of introgressive hybridization with introduced rainbow trout (O. mykiss, RBT) and the genetic structure of hybridizing populations in the upper Kootenay River, southeastern British Columbia, Canada. Using four diagnostic nuclear loci we calculated a hybrid index, inbreeding coefficient, FIS, and the linkage disquilibrium correlation coefficient, Rij, for each locality to determine the distribution of genotypes in each population. We also categorized the 142 hybrid individuals found across localities into four hybrid classes based on their genotypes. The majority of localities (11/18) showed a unimodal distribution of genotypes skewed towards genotypes of WCT. Two localities, however (lower Gold Creek and Lodgepole Creek) showed a flat to bimodal distribution and one site (lower Bull River) showed a unimodal distribution skewed towards RBT genotypes. The majority of hybrid individuals were classified genotypically as WCT backcrosses (59%) and post-F1 individuals (24%). We found a skewed ratio of pure WCT to pure RBT (17:1) and only four F1 hybrids (3%), suggesting that the spread of RBT alleles may be facilitated by hybrids straying to neighbouring populations. We also tested for the action of selection in one population using cohort analyses, but found little evidence of differential selection between pure WCT and hybrid individuals. Pooled across age classes there were significant differences in genotypic frequencies among loci suggesting differential introgression. There was no asymmetry to the hybridization between rainbow trout and westslope cutthroat trout because both species' mitochondrial DNA haplotypes were observed at similar frequencies in the hybrids. Our analyses suggest that hybrid swarms are likely to form in the upper Kootenay River drainage and that certain native WCT populations in British Columbia are at risk of local genomic extinction.     

HETEROZYGOSITY AND GROWTH IN MARINE BIVALVES: FURTHER DATA AND POSSIBLE EXPLANATIONS

In a natural population of two-year-old mussels, shell length was correlated with degree of heterozygosity. There was no correlation between an individual's glycogen level and its degree of heterozygosity, but when individuals were grouped in heterozygosity classes a near-significant correlation was observed between degree of heterozygosity and mean glycogen level corrected for the effects of sex and stage of gonad development. There was no correlation between degree of heterozygosity and index of gonad development. Such a correlation would have provided support for the hypothesis (Zouros and Foltz, 1984) that dependence of time of spawning on heterozygosity may explain the observed heterozygote-deficiency. The causes of heterozygote-deficiency, a common phenomenon in populations of marine bivalves, remain obscure. The observed heterozygosity-growth correlation is examined in the light of the controversy of whether allozymes act as markers in linkage association with genetic conditions that are responsible for the differences in growth among individuals or are themselves the agents of the correlation. The observations that 1) the contributions of individual loci to the correlation vary among populations, 2) the correlation is observed in samples from natural populations but not among progeny from pair matings, and 3) the correlation is nearly always accompanied with heterozygote-deficiency in the population are more compatible with the first explanation and suggest that the growth-heterozygosity correlation results mostly from associative overdominance and to a lesser extent from the direct contributions of scored loci to growth.     

Genetic Organization and Adaptive Response of Allozymes to Ecological Variables in FUNDULUS HETEROCLITUS

Populations of Fundulus heteroclitus, (Cyprinodontidae) a widespread coastal marine fish, were studied in control and artificially heated environments on the North Shore of Long Island, New York to determine (1) patterns of variation in biochemical phenotypes and (2) the extent to which this variation reflected adaptation to environmental characteristics.—Variation at three of twelve polymorphic isoenzyme loci from the warm water population was beyond the range of variation among control populations, and resembled those determined for populations living at more southern latitudes. Hence, these differences were interpreted as adaptations to warm environments. Significant differences in allele frequencies and zygotic proportions at ten of twelve isoenzyme loci were found associated with differences in environments, sexes, and/or age classes. These data strongly support the view that protein polymorphisms are adaptive.—Several observations suggested that selection acts upon multilocus phenotypes rather than upon those of single loci. Several di-locus phenotypic distributions were demonstrated to be nonrandom, and those that exhibited similar patterns of dependence over years were postulated to be maintained by selection. Highly heterozygous fish exhibited superior viability when cohorts were compared over successive years.—The consequences of the polygynous mating system in this species for maintaining genetic variation and for allowing rapid evolutionary response to a variable environment are discussed.     

瑞士阿尔卑斯山欧洲落叶松居群的遗传变异和分化

应用等位酶分析技术,沿两个海拔梯度在瑞士阿尔卑斯山研究了欧洲落叶松（Larix decidua Mill.)居群内和居群间的遗传多态性,结果表明,多态性位点的比例为22.9%,平均每个位点的等位基因数为1.3,平均期望杂合度为0.095,遗传变异的5.8%存在于居群之间,平均遗传距离为0.006。几个有统计意义的基因频率差别在不同树龄类被发现,正在繁育系数值表明在瑞士阿尔卑斯山欧洲落叶松居群有相当的杂合体缺乏,在阿尔拜特（Ar-pette),海拔最高的亚居群与其他亚居群相比较显示最低的遗传多态性（如显示最低的我态性位点比例和最低的平均期望杂合度）和最大的遗传距离值,在最高亚居群和其他亚居群间的遗传差别暗示奠基效应可能是影响这个定样场所欧洲落叶松居群遗传分化的主要因素。