Frequencies of protan and deutan alleles in some Israeli communities and a note on the selection-relaxation hypothesis

Anomaloscopic diagnoses of red-green vision defects are reported and compared to the Ishihara tests for six Israeli populations. The highest frequencies of defects, about 10%, were found in an Arab sample and among Ashkenazi Jews; the lowest — about 4% — among Yemenite Jews. Heterogeneity was also found regarding the relative frequencies of the different alleles; these differences are due primarily to alleles causing milder defects (particularly deuteranomaly) while frequencies of anopias are rather similar. It seems that the same phenomenon prevails for other population differences as well. These findings are discussed in relation to the hypothesis that present-day high rates of colorblindness in some populations may be explained by the relaxation of selection pressure against colorblindness.     

Incidence of red-green color blindness in the Basque population

The incidence of red-green colour vision defects was studied in a sample of 392 Basque students (174 males and 218 females), using the Ishihara test cards (1987). The frequency of red-green colour blindness was 4.02 percent in the males and 0.46 percent in the females. The colour blindness frequencies found among males are within the range of other Spanish samples. Nevertheless they are lower than the values reported in other European populations.     

Defective colour vision and taste sensitivity to PTC in the Maharashtrian population

Three caste groups of the Maharashtrian population, namely Brahmin (N=58), Maratha (N=989) and Scheduled caste (N=1073), were studied for defective colour vision and for the ability to taste phenylthiocarbamide (PTC). Comparisons of defective colour vision and PTC taste sensitivity were made with other Maharashtrian populations studied previously by various authors. The incidence of defective colour vision is lowest among the Brahmins (3.44%) and highest in the Scheduled caste people (4.28%). Taste sensitivity to PTC is highest among the Brahmins (72.5%) with a value which is close to the Vednagar Brahmins (73.3%) who show the highest frequency of the ‘T’ gene recorded so far in Maharashtra.     

Familial appraisal of colorblindness in school children of an Indian population

A total 2000 unrelated school children were screened for colorblindness in Vishakhapatnam, India. Whether the protan and deutan defects are the result of mutations at one locus or at two loci has not been completely resolved, although the evidence favors two discrete loci. The investigation was extended to the families of the 40 color vision anomalous children to study the descendance patterns of these two loci. The importance of these observations are discussed.     

Genotype-phenotype relationships in human red/green color-vision defects: molecular and psychophysical studies.

The relationship between the molecular structure of the X-linked red and green visual pigment genes and color-vision phenotype as ascertained by anomaloscopy was studied in 64 color-defective males. The great majority of red-green defects were associated with either the deletion of the green-pigment gene or the formation of 5' red-green hybrid genes or 5' green-red hybrid genes. A rapid PCR-based method allowed detection of hybrid genes, including those undetectable by Southern blot analysis, as well as more precise localization of the fusion points in hybrid genes. Protan color-vision defects appeared always associated with 5' red-green hybrid genes. Carriers of single red-green hybrid genes with fusion in introns 1-4 were protanopes. However, carriers of hybrid genes with red-green fusions in introns 2, 3, or 4 in the presence of additional normal green genes manifested as either protanopes or protanomalous trichromats, with the majority being protanomalous. Deutan defects were associated with green-pigment gene deletions, with 5' green-red hybrid genes, or, rarely, with 5' green-red-green hybrid genes. Complete green-pigment gene deletions or green-red fusions in intron 1 were usually associated with deuteranopia, although we unexpectedly found three carriers of a single red-pigment gene without any green-pigment genes to be deuteranomalous trichromats. All but one of the other deuteranomalous subjects had green-red hybrid genes with intron 1, 2, 3, or 4 fusions, as well as several normal green-pigment genes. The one exception had a grossly normal gene array, presumably with a more subtle mutation. Amino acid differences in exon 5 largely determine whether a hybrid gene will be more redlike or more greenlike in phenotype. Various discrepancies as to severity (dichromacy or trichromacy) remain unexplained but may arise because of variability of expression, postreceptoral variation, or both. When phenotypic color-vision defects exist, the kind of defect (protan or deutan) can be predicted by molecular analysis. Red-green hybrid genes are probably always associated with protan color-vision defects, while the presence of green-red hybrid genes may not always manifest phenotypically with color-vision defects. Four subjects who were found to have 5' green-red hybrid genes in addition to normal red- and green-pigment genes had normal color vision as determined by anomaloscopy. These were discovered among a group of 129 Caucasian males who had been recruited as volunteers for a vision study.(ABSTRACT TRUNCATED AT 400 WORDS)     

Ugandan colorblinds revisited

A rapid examination with the Ishihara plates of secondary schoolboys in Kampala was followed by anomaloscopy of those who failed or hesitated on the screening test. The average rate of all red-green deficiencies among 1626 lads of various Bantu and Nilotic origins is 3.9%. This is twice a previous estimate, obtained by methods which apparently failed to detect anomalous trichromates. An exceptionally high rate of defects (13.8%) and particularly of deuteranopia (7.3%) was found in a sample of 261 Ismailites. The average rate of all defects among 288 boys of other Indian and Pakistani communities is 4.5%, which is not significantly different from the rate found among Africans. Deutan/protan ratio among indigenous Ugandan colorblinds is 1.07, considerably lower than the ratio of Europeans and Asians. Africans' rate of dichromatic red-green blindness, 2.5%, is at about the average found elsewhere.     

Molecular patterns and sequence polymorphisms in the red and green visual pigment genes of Japanese men

The red-green pigment gene arrays of 203 (101 from a previous study and 102 from this study) randomly selected men of Japanese ancestry from the Seattle area were screened for the abnormal molecular patterns (deletions and red/green or green/red hybrid genes) that are usually associated with defective color vision. Such molecular patterns were found in approximately 5% of these individuals, which is equivalent to the frequency of phenotypic color vision defects in Japanese males in Japan. Thus, the majority of hybrid genes carried by Japanese males appear to be associated with defective color vision. In contrast, the frequency of hybrid genes among Caucasians and African-Americans is approximately two and five times the frequency of color vision defects in these two ethnic groups, respectively. The coding sequences of 50 males of Japanese ancestry were determined. All the polymorphisms in the red and green pigment genes that were detected in the Japanese sample had been observed in Caucasians and African-Americans. The same polymorphisms of the red pigment gene were present in the green pigment gene, suggesting that gene conversion contributes to sequence homogenization between these pigment genes. As is the case for Caucasians, exon 3 of the red and green pigment genes was observed to be a hot spot for recombination and gene conversion. Fewer polymorphic sites (4 vs 11) and haplotypes (5 vs 14) of the red pigment gene were observed in Japanese than in Caucasians. The Japanese population was more uniform with respect to the red pigment gene, with 70% of individuals having the same haplotype, as compared with the 43% for the Caucasian population. This difference was largely due to the lower degree of polymorphism at position 180 of the red pigment gene in Japanese (84% Ser and 16% Ala vs 62% Ser and 38% Ala.) The number of polymorphic sites and haplotypes in the green pigment gene was similar in the two populations. Nevertheless, the Japanese population was more uniform with 65% having the same haplotype. The difference in the frequency of alleles at position 283 accounted for this difference in haplotype distribution.     

High-density single-nucleotide polymorphism maps of the human genome

Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans as part of The SNP Consortium's Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency > or =10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the several percentage point allele frequency differences among the closely related Korean, Japanese, and Chinese populations suggest caution in using mixtures of well-established populations for case-control genetic studies of complex traits. We estimate that approximately 7% of these SNPs are private SNPs with minor allele frequencies <1%. A useful set of characterized SNPs with large allele frequency differences between populations (>60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available.     

The apolipoprotein E polymorphism: a comparison of allele frequencies and effects in nine populations.

Application of uniform methods for measuring the apolipoprotein (apo) E polymorphism and plasma cholesterol levels in nine populations (Tyrolean, Sudanese, Indian, Chinese, Japanese, Hungarian, Icelandic, Finnish, and Malay) revealed significant heterogeneity among them in apo E type frequencies and mean cholesterol levels. The major apo E types in all populations were E3/2 (frequency range from 7.0% in Indians to 16.9% in Malays), E3/3 (frequency range from 39.8% in Sudanese to 72.1% in Japanese), and E3/4 (frequency range from 11.3% in Japanese to 35.9% in Sudanese). Mean cholesterol levels ranged from 144.2 mg/dl in the Sudanese to 228.5 mg/dl in the Icelandics. Two-way analysis of variance of the effect of population and apo E type on cholesterol levels showed no significantly interaction effect, indicating that the effects of apo E type on cholesterol levels do not differ significantly among the populations. The overall average excess for the epsilon 2 allele was -14.12 mg/dl (range -31.63 to -8.82 mg/dl); for the epsilon 3 allele, 0.04 mg/dl (range -1.87 to 1.58 mg/dl; and for the epsilon 4 allele, 8.14 mg/dl (range -1.71 to 13.31 mg/dl). Despite the apparent heterogeneity in these values, especially for the epsilon 4 allele, comparison of the average excesses by a method of repeated sampling with random permutations revealed no significant difference in effects among populations. These data indicate that a given apo E allele acts in a relatively uniform manner in different populations despite differences in genetic background and environmental factors.     

Population Structure of Wild Musk Shrews (Suncus murinus) in Asia Based on Mitochondrial DNA Variation, with Research in Cambodia and Bhutan

The musk shrew (Suncus murinus) is a small mammalian species belonging to Insectivora. It is widely distributed in Asia. To identify the genetic relationship among wild musk shrew populations and examine its migration route, we investigated the populations of Cambodia and Bhutan by using mitochondrial DNA restriction fragment length polymorphism analysis and compared them with other Asian populations previously described. Four haplotypes were detected in Cambodia and eight in Bhutan. A total of 53 haplotypes were detected in Asia and were classified largely into two groups, the Continental and Island types, based on a minimum spanning network. From the distribution of mtDNA types in wild musk shrews, three major population groups are identified in Asia: South Asia, Southeast Asia, and Malay. It is suggested that the Malay population group was a mix of South and Southeast Asian population groups and that this was a contact area of the two groups. In addition, other contact areas between the South and Southeast Asian groups exist in Myanmar, but unlike the Malay, the Myanmar area was the border of these groups.     

Linkage Disequilibrium for Two X-Linked Genes in Sardinia and Its Bearing on the Statistical Mapping of the Human X Chromosome

The distribution of four X-linked mutants (G6PD, Deutan, Protan and Xg) among lowland and once highly malarial populations of Sardinia discloses a clear-cut example of linkage disequiligrium between two of them (G6PD and Protan). In the same populations the distribution of G6PD-deficiency versus colorblindness of the Deutan type and the Xg blood-group is not significantly different from that expected at equilibrium. These data suggest indirectly that the loci for G6PD and Protan may be nearer to one another than those for G6PD and Deutan.     

Psychophysical Evaluation of Congenital Colour Vision Deficiency: Discrimination between Protans and Deutans Using Mollon-Reffin’s Ellipses and the Farnsworth-Munsell 100-Hue Test

We have used the Farnsworth-Munsell 100-hue (FM 100) test and Mollon-Reffin (MR) test to evaluate the colour vision of 93 subjects, 30.4 ± 9.7 years old, who had red-green congenital colour vision deficiencies. All subjects lived in Belém (State of Pará, Brazil) and were selected by the State of Pará Traffic Department. Selection criteria comprised the absence of visual dysfunctions other than Daltonism and no history of systemic diseases that could impair the visual system performance. Results from colour vision deficient were compared with those from 127 normal trichromats, 29.3 ± 10.3 years old. For the MR test, measurements were taken around five points of the CIE 1976 colour space, along 20 directions irradiating from each point, in order to determine with high-resolution the corresponding colour discrimination ellipses (MacAdam ellipses). Three parameters were used to compare results obtained from different subjects: diameter of circle with same ellipse area, ratio between ellipse’s long and short axes, and ellipse long axis angle. For the FM 100 test, the parameters were: logarithm of the total number of mistakes and positions of mistakes in the FM diagram. Data were also simultaneously analysed in two or three dimensions as well as by using multidimensional cluster analysis. For the MR test, Mollon-Reffin Ellipse #3 (u’ = 0.225, v’ = 0.415) discriminated more efficiently than the other four ellipses between protans and deutans once it provided larger angular difference in the colour space between protan and deutan confusion lines. The MR test was more sensitive than the FM 100 test. It separated individuals by dysfunctional groups with greater precision, provided a more sophisticated quantitative analysis, and its use is appropriate for a more refined evaluation of different phenotypes of red-green colour vision deficiencies.     

Ethnic variations of a retinoblastoma susceptibility gene (RB1) polymorphism in eight Asian populations

An A → G single nucleotide polymorphism (SNP) at nucleotide 153,104 in the retinoblastoma susceptibility locus (RB1) at 13q14 was previously reported to be present only in Asians. In this study, we determined the distribution of this SNP in normal Southeast Asian populations (Chinese, Malay, Javanese, Thai, Filipino), in South Asian populations (Bangladeshi, Pakistani Pushtun and Indian) and in Chinese retinoblastoma cases and control subjects. TheRB1 SNP was present in all populations at an overall frequency of ≤0.18. Heterozygosity was higher in the Southeast Asian groups (0.14–0.34) than in the South Asian groups (Bangladeshi and Indian) (0.04–0.06). Significant differences in allele frequencies were found between the two population groups. Interestingly, our Pakistani population comprised of ethnic Pushtuns from northwest Pakistan was significantly different from the neighbouring Bangladeshi and Indian populations. No significant difference was found between Chinese case patients and control subjects. ThisRB1 SNP appears to be an ethnic variant prevalent in Southeast Asian populations and may be useful for studyingRB1 inheritance by pedigree analysis.     

Respiration-deficient Chinese hamster cell mutants: genetic characterization.

We present here genetic experiments with a series of Chinese hamster cell mutants defective in oxidative energy metabolism. The mutations were all shown to be recessive in intraspecies hybrids. Thirty-five mutants were sorted into eight complementation groups, but one of these mutants failed to complement representatives of two distinct complementation groups. The possibility was raised that this is a cell carrying two mutations or a deletion. Because of the greatly different frequencies with which such mutants could be isolated from two different Chinese hamster cell lines, CCL16 (DON) and V79, the stability of representatives from each cell line was examined, and it was found that revertants could be obtained after treatment with mutagens, while spontaneous revertants appeared at unmeasurable or extremely low frequencies, with one exception. The mutant with a very noticeable frequency of spontaneous reversion was defective in mitochondrial protein synthesis, and the question arose whether the mutation was on the mitochondrial genome. A detailed fluctuation analysis of reversion rate and comparison with rates for other mutations was consistent with a nuclear mutation. This conclusion was supported by experiments involving fusions with cytoplasts.     

Chromosomal instability in mutagen-sensitive mutants isolated from mouse lymphoma L5178Y cells. I. Five different genes participate in the formation of baseline sister-chromatid exchanges and spontaneous chromosomal aberrations

In a search for cell mutants that show an increase or a decrease in the frequency of baseline sister-chromatid exchanges (SCEs) or spontaneous chromosomal aberrations (CAs), large numbers of mutagen-sensitive clones previously isolated from mouse lymphoma L5178Y cells were analyzed. In addition to two SCE mutants (ES 4 and AC 12) previously reported, three other mutants were identified as an SCE mutant. An ethyl methanesulfonate-sensitive mutant ES 2 and an alkylating agent-sensitive mutant MS 1 exhibited, respectively, 1.4-fold and 1.8-fold higher baseline SCE frequencies than did the parental L5178Y. In contrast, M10, which is sensitive to X-ray and 4-nitroquinoline 1-oxide, showed a reduced frequency of baseline SCEs (0.65-fold). These 5 mutants including ES 4 and AC 12 had 3--9-fold increases in spontaneous CA frequencies. Measurement of baseline SCE formation in inter-mutant hybrids revealed that M10 mutation is dominant, MS 1 and ES 4 mutations are semidominant, and ES 2 and AC 12 mutations are recessive. Because SCE frequencies in hybrids formed between pairs of 4 mutants (ES 2, MS 1, ES 4 and AC 12) were significantly lower than those in the tetraploid mutant cells, these 4 mutants probably belong to different complementation groups. Since M10 behaved dominantly with respect to SCE phenotype, it was not possible to determine by complementation test whether it belongs to a different group from the other mutants. However, the finding that M10 is complemented by other mutants for EMS sensitivity indicates that the M10 mutation is different from the other mutations. From these results, it is concluded that at least 4 different genes participate in the formation of high levels of baseline SCEs. The defects in ES 2, MS 1, ES 4, and AC 12 produce common lesions responsible for the formation of both SCEs and CAs. In contrast, the defect in M10 is associated with a high increase in spontaneous CA frequency, but conversely associated with a decrease in baseline SCE frequency. This suggests that M10 is defective in the process involved in the formation of baseline SCEs.     

HSM2 (HMO1) gene participates in mutagenesis control in yeast Saccharomyces cerevisiae

We have previously reported about a new Saccharomyces cerevisiae mutation, hsm2-1, that results in increase of both spontaneous and UV-induced mutation frequencies but does not alter UV-sensitivity. Now HSM2 gene has been genetically and physically mapped and identified as a gene previously characterized as HMO1, a yeast homologue of human high mobility group genes HMG1/2. We found that hsm2 mutant is slightly deficient in plasmid-borne mismatch repair. We tested UV-induced mutagenesis in double mutants carrying hsm2-1 mutation and a mutation in a gene of principal damaged DNA repair pathways (rad2 and rev3) or in a mismatch repair gene (pms1 and recently characterized in our laboratory hsm3). The frequency of UV-induced mutations in hsm2 rev3 was not altered in comparison with single rev3 mutant. In contrast, the interaction of hsm2-1 with rad2 and pms1 was characterized by an increased frequency of UV-induced mutations in comparison with single rad2 and pms1 mutants. The UV-induced mutation frequency in double hsm2 hsm3 mutant was lower than in the single hsm2 and hsm3 mutants. The role of the HSM2 gene product in control of mutagenesis is discussed.     

Concomitant loss of transforming growth factor (TGF)-beta receptor types I and II in TGF-beta-resistant cell mutants implicates both receptor types in signal transduction

A panel of 71 chemically mutagenized Mv1Lu mink lung epithelial cell clones were selected based on their resistance to the growth inhibitory action of transforming growth factor beta 1 (TGF-beta 1) and TGF-beta 2. Characterization of TGF-beta receptors in these mutants indicates that the TGF-beta-binding membrane proteoglycan, betaglycan, is apparently normal in all of them. However, 14 of the mutant clones are defective in TGF-beta receptor type I, and 22 clones are simultaneously defective in receptor types I and II. The clones with type I receptor defects fall into two distinct phenotypes, called R and LR. The R phenotype is characterized by the lack of detectable type I receptors, and has been previously described (Boyd, F. T., and Massagué, J. (1989) J. Biol. Chem. 264, 2272-2278). LR mutants are characterized by expression of low levels of type I receptor and are, like the R mutants, completely resistant to growth inhibition by TGF-beta 1 or -beta 2. Mutant clones that are simultaneously defective in receptor types I and II fall into three distinct phenotypes. These included DRa mutants which are characterized by lack of detectable receptor types I and II, DRb mutants which are characterized by low expression of both receptor types and an anomalously fast electrophoretic mobility of the type II receptor protein. All mutants that have a low level of type II receptor are also defective in type I receptor. In addition to the loss of growth inhibitory response, the receptor-defective mutants described here have lost all other responses to TGF-beta 1 and -beta 2 known to occur in parental Mv1Lu cells. The defects present in these mutant clones are not encountered in clones isolated from nonmutagenized parental Mv1Lu cells or in mutagenized cells that had not been exposed to selection with TGF-beta. The results implicate TGF-beta receptor types I and II in the mediation of a common set of cellular responses to TGF-beta. Furthermore, the high relative frequency of isolation of DR mutants raises the possibility that receptor types I and II interact as part of a common signaling TGF-beta receptor complex.     

Spatiochromatic properties of natural images and human vision

The human visual system shows a relatively greater response to low spatial frequencies of chromatic spatial modulation than to luminance spatial modulation. However, previous work has shown that this differential sensitivity to low spatial frequencies is not reflected in any differential luminance and chromatic content of general natural scenes. This is contrary to the prevailing assumption that the spatial properties of human vision ought to reflect the structure of natural scenes. Now, colorimetric measures of scenes suggest that red-green (and perhaps blue-yellow) color discrimination in primates is particularly suited to the encoding of specific scenes: reddish or yellowish objects on a background of leaves. We therefore ask whether the spatial, as well as chromatic, properties of such scenes are matched to the different spatial-encoding properties of color and luminance modulation in human vision. We show that the spatiochromatic properties of a wide class of scenes, which contain reddish objects (e.g., fruit) on a background of leaves, correspond well to the properties of the red-green (but not blue-yellow) systems in human vision, at viewing distances commensurate with typical grasping distance. This implies that the red-green system is particularly suited to encoding both the spatial and the chromatic structure of such scenes.     

Genetic Structure of the Ancestral Population of Modern Humans

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n= 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The ``age before fixation' of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n= 860 chromosomes in total). Seventeen polymorphisms older tan 100,000–200,000 years, which contributed ∼90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000–200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period. Received: 3 February 1998 / Accepted: 9 February 1998     

Immunoglobulin (GM and KM) allotypes in the Sikh population of India

The populations of India are genetically diverse, both within and between geographic regions; immunoglobulin (GM) allotypes provide important information on genetic differences between populations, since the frequencies of combinations of allotypes (termed "haplotypes") vary dramatically among ethnic groups. As part of a project to assess genetic diversity among defined Indian populations, we have examined eight GM allotypes in a sample of 101 unrelated Sikhs who have migrated to Toronto, Canada: Glm(1, 2, 3, 17) and G3m (5, 15, 16, 21). Sikhs are a religious group that arose in the Punjab about 1500 A.D.; most of the original converts are believed to have been middle to upper-middle caste Hindus. Gm allotyping showed that six Gm haplotypes occurred at polymorphic frequencies (greater than 0.01) in Sikhs: Gm3;5, Gm1,17;21, Gm1,2,17;21, Gm1,17;5, Gm1,17;15,16, and Gm1,3;5. These haplotypes have all been previously reported in Indian populations. The frequencies of the first four haplotypes resembled the published frequencies for lower-caste Hindus of NW India more than upper-caste Hindus. However, the last two haplotypes have been found only in upper-caste Hindus. The frequency of one of these, Gm1,17;15,16 was higher in Sikhs (0.09) than has been reported in any Indian population with the exception of Parsis (who are descended from Iranians). We speculate that the high frequency of this haplotype may have been characteristic of some of the Hindu castes in the Punjab from which Sikhs are descended.