Population genetics study of differential fertility in humans (based on an example of habitual abortion). III. Distribution of individual heterozygosity and genotype combinations for 9 polymorphic loci

Distribution of individual heterozygosity (the number of heterozygous loci per individual), wife/husband genetical differences and frequencies of genotypes formed by paired combination of eight polymorphic loci were studied in a group of couples and single women with repeated spontaneous abortions, and in a group of couples with normal fertility. No statistically significant differences were found for the first two parameters. Marked increase of genetical variability was shown for the women with repeated spontaneous abortions, as consequence of elevation of frequency of rare genotypic paired combinations. Therefore, differential fertility, as a component of stabilizing selection, alters the distribution of complex genotypes in human populations.     

Population genetic study of differential fertility in man (illustrated by habitual abortion). IV. Distribution of blood groups and frequency of incompatible marriages

Hereditary variation of 5 immunological systems coded by 8 loci was compared in 148 couples and 100 women with repeated spontaneous abortions in anamnesis (experimental group) and 141 couples and 100 women with normal fertility (control group). Marked differences in distributions of genotypes and frequencies of 3 systems (MNSs, Rhesus, Duffy) and frequency of AB0-incompatible couples were found between control and experimental groups. An average value of observed heterozygosity in experimental group was lower, as compared to the expected value. Possible influence of immunological factors on recurrent fetal wastage is discussed.     

Population genetic study of differential fertility in man (illustrated by habitual abortion). V. Distribution of individual heterozygosity and parameters of genotypic variability for a set of immunological genetic markers

Distribution of individual heterozygosity (the number of heterozygous loci per individual), frequencies of genotypes formed by paired combinations of 5 loci and values of linkage disequilibrium between 6 blood group loci were studied both in a group of couples and single women with recurrent abortions in anamnesis, and in a group of couples and single women with normal fertility. Statistically significant deficit of highly heterozygous individuals was found in the experimental group. Marked increase of genetical variability was shown for the women with repeated abortions, as a consequence of elevation of rare genotypic paired combination frequency. Therefore, differential fertility as a component of stabilizing selection alters the distribution of complex genotypes in human populations. Differences in values of linkage disequilibrium between women with repeated abortions and those of normal fertility were not found.     

Algebraic regularities of the ratio of heterozygosity with a mean and variance of quantitative character

The relationships of heterozygosity with the mean and variance of quantitative character were considered under neutrality, additivity and overdominance of polymorphic loci. Attention was drawn to dependence of the patterns of relationships on the number of polymorphic loci (which varied from 1 to 10) and on the type of polymorphic loci, both homogeneous (polymorphic loci are of the same type) and heterogeneous (polymorphic loci are of the two types) samples of 10 polymorphic loci and their combination. It is shown that increase in the number of polymorphic loci is accompanied with extension of the limits of corresponding relations, whereas the patterns of these relations depend on the type of connection of separate polymorphic locus with the quantitative character and on the ratio of different loci in the set of polymorphic loci. It is assumed that the relationship of heterozygosity with quantitative characters, displayed in the number of experimental works, may contain a component mediated by similar statistical effects. It is inferred that the discrepancy between different authors' experimental data on existence or lack of some relationships between multiplicative heterozygosity and morphological variability of quantitative characters can be explained by different types of relations of polymorphic loci to quantitative characters encountered in their works.     

Negative correlation between heterozygosity and potential fertility in the Eveny population of Iakutiia

The relationship between heterozygosity of 9 polymorphic loci and fertility of women surviving beyond the menopause was studied in the North-Siberian tribe Eveny. The number of pregnancies negatively correlated with the individual heterozygosity (r = -0.2913 + 0.1302, P less than 0.05). Drastic fertility reduction in heterozygous women was observed for G1M, ACP and HP loci.     

中国朝鲜族9个STR基因座遗传多态性研究

为丰富中华民族基因数据库,获取中国吉林省特有少数民族--朝鲜族D3S1358、vWA、FGA、TH01、TPOX、CSF1PO、D5S818、D13S317、D7S820等9个STR基因座的群体遗传数据。采用四色荧光标记STR基因扫描技术,检测91个无关个体血液样本。结果共检出81种等位基因,其基因频率分布在0.0055~0.4615之间;共检出196种基因型,其基因型频率分布在0.0110~0.9890之间。9个STR基因座基因型频率观察值与期望值均符合Hardy-Weinberg平衡定律（P＞0.05）。9个基因座的多态信息量PIC（polymorphic information content）分布于0.6863~0.8807之间,杂合度H（heterozygosity）分布于0.6919~0.8809之间,个体识别力DP（discrimination power）分布于0.8301~0.9670之间,非父排除率PPE（probability of paternity exclusion）分布于0.8590~0.9942之间。研究结果可应用于人类群体遗传学及法医学研究等领域。 Genetic Polymorphism of 9 STR loci in Chaoxian National Minority of China GAO Ya1,JIN Tian-bo1,LAI Jiang-hua1,CHEN Teng1,ZHENG Hai-bo1,ZHU Bo-feng1,HU Song-nian2,WANG Jian2,LI Sheng-bin1 1.Forensic Laboratory of Ministry of Health of Xi'an Jiaotong University,710061,Xi'an China; 2.Beijing Huada Genomics Institute( Beijing Airport Industrial Zone B-6),101300,Beijing,China Abstract:In order to enrich the Chinese genetic database,nine polymorphic loci of STR,such as D3S1358,vWA,FGA,TH01,TPOX,CSF1PO,D5S818,D13S317 and D7S820 were studied.Based on STR gene scan marked by fluorescence,91 unrelated Chinese Chaoxian individuals were observed.81 alleles and 196 genotypes were found.The corresponding gene frequency and genotype frequency were 0.0055~0.4615 and 0.0110~0.9890 respectively.The genogypes frequency of nine STR loci was good with the Hardy-Weinberg equilibrium（P＞0.05）.The statistical analysis of nine STR loci showed the following：PIC（polymorphic information content）≥0.6863,H（heterozygosity）≥0.6919,DP（discrimination power）≥0.8301,EPP（probability of paternity exclusion）≥0.8590.The data studied can be used in Chinese population genetic studies and forensic medicine applications. Key words：Chaoxian groups of China;STRs;gene scan;genetic polymorphism     

Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks

Evolutionary and conservation biologists often use molecular markers to evaluate whether populations have experienced demographic bottlenecks that resulted in a loss of genetic variation. We evaluated the utility of microsatellites for detection of recent, severe bottlenecks and compared the amounts of genetic diversity lost in bottlenecks of different sizes. In experimental mesocosms, we established replicate populations by releasing 1, 2, 4 or 8 pairs of the western mosquitofish, Gambusia affinis (Poeciliidae). Using eight polymorphic microsatellite loci, we quantified seven indices of genetic diversity or change that have been used to assess the effects of demographic bottlenecks on populations. We compared indices for the experimentally bottlenecked populations to those for the source population and examined differences between populations established with different numbers of founders. Direct count heterozygosity and the proportion of polymorphic loci were not very sensitive to genetic changes that resulted from the experimental bottlenecks. Heterozygosity excess and expected heterozygosity were useful to varying degrees in the detection of bottlenecks. Allelic diversity and temporal variance in allele frequencies were most sensitive to genetic changes that resulted from the bottlenecks, and the temporal variance method was slightly more correlated with bottleneck size than was allelic diversity. Based on comparisons to a previous study with allozymes, heterozygosity, temporal variance in allele frequencies and allelic diversity, but not proportion of polymorphic loci, appear to be more sensitive to demographic bottlenecks when quantified using microsatellites. We found that analysis of eight highly polymorphic loci was sufficient to detect a recent demographic bottleneck and to obtain an estimate of the magnitude of bottleneck severity.     

我国地方鸡品种保种群微卫星多态性分析与分子标记档案的建立

利用20个微卫星标记对国家家禽品种资源基因库中保存的11个地方鸡品种保种群进行了遗传检测,计算各群体的等位基因频率、平均基因杂合度、平均多态信息含量及各群体间的遗传距离,并用类平均法进行聚类分析。研究结果表明：20个微卫星标记在11个地方鸡品种保种群共检测到176个等位基因,平均为8.8个,基因频率分布在0.013～0.838之间。检测到等位基因中,有45个等位基因为11个地方鸡品种所共有;11个地方鸡品种平均杂合度在0.6800～0.7432之间。其中藏鸡最高,为0.7432;狼山鸡最低,为0.6800;平均多态信息含量在0.6329～0.7023之间,均大于0.5,表现为高度多态性;11 个鸡品种聚为4类。丝羽乌骨鸡、茶花鸡、仙居鸡、藏鸡、萧山鸡聚为一类,鹿苑鸡、狼山鸡聚为一类,固始鸡、北京油鸡、大骨鸡聚为一类,河南斗鸡单独聚为一类;通过利用20个微卫星基因座检测不同世代群体中等位基因及其频率、群体基因平均杂合度和多态信息含量,建立地方鸡品种保种群微卫星标记档案,并分析世代间的差异,预期可以达到监测保种效果的目的。     

Isolation and characterization of 16 microsatellite loci in the humbug damselfish, Dascyllus aruanus (family Pomacentridae)

Here we report on 16 microsatellite loci designed for the damselfish Dascyllus aruanus. All loci were tested on 98 individuals and were polymorphic (seven to 35 alleles). Expected heterozygosity ranged from 0.705 to 0.942. Six loci showed Hardy-Weinberg disequilibrium due to the occurrence of null alleles. Cross-species amplifications conducted within the genus Dascyllus (D. carneus, D. strasburgi, D. trimaculatus) lead to polymorphic fragments in 32 out of 48 tests. These 16 loci will enable future research into the behavioural ecology and population ecology of Dascyllus aruanus throughout the Indo-Pacific.     

9号染色体短臂上7个STR基因座在基因扫描中的信息表现

为了初步探讨7个位于染色体9p区域的短串联重复序列(shorttandemrepeat,STR)基因座:D9S288、D9S157、D9S1748、D9S171、D9S161、D9S1817和D9S1805在遗传学研究及法医学应用中的意义,随机抽取225名湖南汉族无关个体,复合PCR技术扩增上述基因座,ABI377全自动测序仪进行基因分型,共检出75种等位基因,通过对基因型及等位片断频率分布的研究和数据统计分析,7个基因座基因频率分布在0.002～0.800之间,构成243种基因型。7个STR基因座基因型分布均符合Hardy Weinberg平衡定律(P>0.05),杂合度(heterozygosity,H)介于0 347～0.844之间,个体识别力(discriminationpower,DP)为0.346～0.841,非父排除率(probabilitiesofpaternityexclusion,PPE)为0.308～0.738,多态信息含量(polymorphicinformationcontent,PIC)在0.328～0.822之间。种族比较结果显示,湖南汉族与非洲黑人及欧洲白人在大多数基因座均存在显著差异(P<0.001)。研究结果丰富了中华民族基因数据库,在人类群体遗传学及法医学研究领域有重要应用价值。     

Human Population Genetic Studies Using Hypervariable Loci. I. Analysis of Assamese, Australian, Cambodian, Caucasian, Chinese and Melanesian Populations

Population genetic studies, in Australian, Assamese, Cambodian, Chinese, Caucasian and Melanesian populations, were performed with several highly polymorphic DNA loci. Results showed that the Caucasian and Chinese had the highest level of heterozygosity. The size range of the majority of the polymorphic DNA fragments of a locus was the same in the different populations. The distinguishing feature of each ethnic group was the relative frequency of a particular set or group of alleles. For example, alleles greater than 9.0 kb in size, in D14S13, or from 4.5 to 4.7 kb, in D18S27, were less than half as frequent in Caucasians than in the other populations. Overall, there were groups of alleles, at one or more loci, whose frequencies were different among some of the ethnic groups and therefore could be used to differentiate one group from the other.     

Development of microsatellite markers for the bracken fern, Pteridium aquilinum

We isolated eight novel polymorphic microsatellite loci from Pteridium aquilinum. These loci were characterized in 30 individuals, one from Bolivia, two from Peru, one from the USA, one from Japan, and 25 from Northeast China to Southwest China. The number of alleles per locus ranged from two to seven. The observed heterozygosity (H(O) ) ranged from 0.000 to 0.600 with an average of 0.3051, and the expected heterozygosity (H(E) ) ranged from 0.0966 to 0.7780 with an average of 0.4267. One locus deviated from Hardy-Weinberg equilibrium and four pairs of loci were found to be in linkage disequilibrium. These polymorphic loci will be useful in the study of the population genetic structure of Pteridium.     

Microsatellite markers for the endangered root holoparasite Dactylanthus taylorii (Balanophoraceae) from 454 pyrosequencing

? Premise of the study: Microsatellite loci were isolated and developed as polymorphic markers for the New Zealand endemic root holoparasite Dactylanthus taylorii for use in population and conservation genetics studies. ? Methods and Results: Shotgun 454 pyrosequencing was performed on genomic DNA pooled from three individuals of D. taylorii. From 61709 individual sequence reads, primers for 753 microsatellite loci were developed in silico and 72 of these were tested for consistent amplification and variability. Ten microsatellite loci were found to be polymorphic and consistently scorable when screened in 44 individuals from five geographically distant populations. The number of alleles per locus ranged from four to 16 with an average of 9.7, and average observed heterozygosity per locus was between 0.182 and 0.634. ? Conclusions: These polymorphic microsatellite markers establish an important resource for ongoing conservation initiatives and planned population genetic studies of D. taylorii.     

Isolation and characterization of 30 polymorphic microsatellite loci from the mycophagous fly Drosophila innubila

Drosophila innubila is a mushroom-feeding member of the quinaria group, found in the woodlands and forests of the 'sky islands' in Arizona and New Mexico and extending south into central Mexico. Here, we describe and characterize 30 polymorphic microsatellite loci from D. innubila collected in the Chiricahua Mountains in Arizona. The number of alleles ranged from three to 21, and observed heterozygosity ranged from 0.0513 to 0.9737. Six loci were putatively X-linked, six departed from Hardy-Weinberg equilibrium, seven had evidence of null alleles, and six showed evidence of linkage disequilibrium. These markers will be useful for examining population structure of D. innubila and its association with male-killing Wolbachia.     

Electrophoretic variability in natural populations of Drosophila melanogaster and Drosophila simulans

Genetic variation at 59 gene loci coding for enzymes (50) and larval proteins (9) has been studied in sympatric populations of Drosophila melanogaster and D. simulans from insular and continental origin. The average number of alleles per locus, the mean proportion of polymorphic loci and the mean heterozygosity are similar both within and between species. There are however some significant differences between D. simulans populations in the genotypic frequencies for four polymorphic loci.     

Relation between heterozygosity and fertility in Forest Nentzy and Nganasan tribes

The relationship between heterozygosity for 13 polymorphic loci and fertility of women having passed the menopause was studied in two North-Siberian tribes: Forest Nentzy (N = 108) and Nganasans (N = 68). The number of pregnancies positively correlated with the individual heterozygosity (r = 0.2910 +/- 0.1063; P less than 0.01) in Forest Nentzy, while in Nganasans this correlation was absent. Women with the average level of individual heterozygosity were characterized by minimal values of variation in pregnancies' number and maximal Q index of realized fertility. It is concluded that the average level of individual heterozygosity is optimal for both tribes.     

Isolation and characterization of microsatellite loci in Piaractus mesopotamicus and their applicability in other Serrasalminae fish

The subfamily Serrasalminae (Characidae, Teleostei) is an endemic Neotropical group of fishes distributed along the Amazon, Paraná‐Paraguay and Orinoco Basins. The pacu (Piaractus mesopotamicus) is found in all major rivers that comprise the Pantanal of Mato Grosso. In order to investigate population genetic structure within the group, an enriched microsatellite library was constructed. Eight polymorphic were loci screened, with an average of 6.5 alleles per locus. Five loci exhibited greater than 60% heterozygosity. Additionally, a high level of cross‐species amplification was obtained.     

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.     

Microsatellite loci for the southern pine beetle (Dendroctonus frontalis) and cross‐species amplification in Dendroctonus

We developed microsatellite loci for the southern pine beetle (Dendroctonus frontalis). Twelve microsatellite loci were identified. Eight loci were polymorphic and sufficiently variable in 62 individuals (expected heterozygosity ranged from 0.707 to 0.880) to investigate population structure. All loci conformed to HWE except Dfr‐14, which showed heterozygote excess, and no two loci deviated from linkage equilibrium. The loci were tested for cross‐species amplification in four species of Dendroctonus (D. valens, D. terebrans, D. brevicomis, and D. ponderosae). Seven loci were polymorphic in at least one of the species tested.     

Evaluation of genetic variability of the Kamchatka crab Paralithodes camtschaticus (Tilesius) using allozyme markers

Interspecific genetic variation in populations of red king crab Paralithodes camtschaticus Tilesius (Litholidae, Decapoda: Crustacea) was examined using allozyme markers. The activity of 57 enzymes and the general protein presumably encoded by 92 loci was detected. The level of allozyme variability was low: the expected heterozygosity and the proportion of polymorphic loci were respectively 0.027 +/- 0.008 and 6.5%. This level of heterozygosity is three times lower than the average value for 122 crustacean species (0.082 +/- 0.007). Although genetic variants were found at 22 loci, their frequencies were generally low: only in loci 6-Pgd, Alp-1, and Pep-1 did the frequencies of the most common alleles not exceed 0.9. All polymorphic loci except one had two alleles; the exception was 6-Pgd, which had three alleles. The possible reasons for the low level of allozyme variability in red king crab are discussed.