PMC:1271393 / 19213-23106
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1271393","sourcedb":"PMC","sourceid":"1271393","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1271393","text":"The allelic composition of CD209 and CD209L haplotypes and their frequency distribution in the three major ethnic groups is illustrated in figure 2 , along with the haplotype composed of the ancestral allelic state of each SNP inferred from chimpanzee data. For CD209, we identified 42 different haplotypes, with an overall heterozygosity of 84% (table 2 ). Three major haplotypes (H2, H29, and H40) accounted for ∼50% of the African variability, whereas they were at very low frequency (H2 at ∼5%) or absent (H29 and H40) in Europeans and East Asians (fig. 2A). In turn, the two haplotypes (H1 and H3) that accounted for 58% and 83% of the European and East Asian variability, respectively, were observed at very low frequency (H1 at 6%) or even absent (H3) in Africa. However, H3, which had a frequency of 36% and 20% in Europe and East Asia, respectively, is just a one-step mutation (SNP 871) from H2, the most frequent haplotype in the African sample. The most interesting observation of the CD209 haplotype variability was the presence of a highly divergent haplotype cluster. This cluster, which contains haplotypes 40–42 (referred to here as “cluster A”), differs from all other haplotypes (referred to here as “cluster B”) by 35 fixed positions (fig. 2A). Cluster A is Africa specific and is present at a frequency of ∼15%, whereas cluster B is present in the remaining African and all non-African samples. It is worth noting that three (SNPs 1839, 1888, and 1908) of the five nonsynonymous mutations identified for this gene are unique to cluster A. In all cases, these three mutations were segregating together, with the exception of one haplotype, H41, which does not contain the SNP 1839. Samples from cluster A are geographically widespread over the entire African continent (i.e., two San from Namibia, three Bantus from Gabon and two from South Africa, three Yorubans from Nigeria, and two Mandenka from Senegal). For CD209L, 74 different haplotypes were observed (fig. 2B), with an overall heterozygosity of 94% (table 2). Only one haplotype (H38) at a frequency of ∼15% was shared in the three continental regions.\nFigure 2 Inferred haplotypes for CD209 (A) and CD209L (B). The chimpanzee sequence was used to deduce the ancestral state at each position, except for the CD209L positions 1232, 1236, and 1240. For those polymorphisms, the ancestral state was considered to be the most frequent allele. Dark boxes correspond to the derived state at each position. The numbers on the right of the figure indicate the absolute frequency of each haplotype in the different populations studied. Repeat-number variation in the neck region of each gene is reported in the gray columns with the column heads “NR.” Indel polymorphisms are referred as to “1” for insertion and “0” for deletion.\nTable 2 Summary of Diversity Indexes and Sequence-Based Neutrality Tests in the Study Populations\nGene and Population No. of Chromosomes No. of Segregating Sites No. of Haplotypes HDa±SD πb ±SD θwc Tajima's D Fay and Wu's H\nCD209:\n African 82 70 26 91.8 ± 1.6 26 ± 3.8 25.3 −.05 −19.45d\n European 86 18 14 79.6 ± 3.0 6.4 ± .6 6.5 −.04 −.26\n East Asian 86 12 11 56.7 ± 5.5 3.3 ± .5 4.3 −.65 −3.82d\n Total 254 79 42 84.5 ± 1.6 13 ± 1.7 23.3\nCD209L:\n African 82 51 40 94.9 ± 1.2 16.1 ± .9 18.7 −.49 −1.52\n European 86 29 23 88.8 ± 1.9 17.7 ± 1.0 10.5 2.01e −.61\n East Asian 86 27 19 86.4 ± 1.8 16.0 ± .5 9.8 1.85d −.43\n Total 254 63 74 93.6 ± .7 17.7 ± .5 18.8\nNote.—\nThe values shown in bold italics correspond to significant values for both the coalescence simulation and the empirical distribution (see the “Material and Methods” section). The analyses considered a total of 5,500 and 5,391 nucleotides for CD209 and CD209L, respectively.\na HD = haplotype diversity (%).\nb Nucleotide diversity per base pair (×10−4).\nc Watterson's estimator per base pair (×10−4).\nd .02\u003cP≤.05.\ne P≤.02.","divisions":[{"label":"figure","span":{"begin":2133,"end":2801}},{"label":"label","span":{"begin":2133,"end":2141}},{"label":"caption","span":{"begin":2142,"end":2801}},{"label":"p","span":{"begin":2142,"end":2801}},{"label":"label","span":{"begin":2802,"end":2809}},{"label":"caption","span":{"begin":2810,"end":2899}},{"label":"p","span":{"begin":2810,"end":2899}},{"label":"table","span":{"begin":2900,"end":3465}},{"label":"tr","span":{"begin":2900,"end":3025}},{"label":"th","span":{"begin":2900,"end":2919}},{"label":"th","span":{"begin":2920,"end":2938}},{"label":"th","span":{"begin":2939,"end":2963}},{"label":"th","span":{"begin":2964,"end":2981}},{"label":"th","span":{"begin":2982,"end":2988}},{"label":"th","span":{"begin":2989,"end":2995}},{"label":"th","span":{"begin":2996,"end":2999}},{"label":"th","span":{"begin":3000,"end":3010}},{"label":"th","span":{"begin":3011,"end":3025}},{"label":"tr","span":{"begin":3026,"end":3032}},{"label":"td","span":{"begin":3026,"end":3032}},{"label":"tr","span":{"begin":3033,"end":3088}},{"label":"td","span":{"begin":3033,"end":3041}},{"label":"td","span":{"begin":3042,"end":3044}},{"label":"td","span":{"begin":3045,"end":3047}},{"label":"td","span":{"begin":3048,"end":3050}},{"label":"td","span":{"begin":3051,"end":3061}},{"label":"td","span":{"begin":3062,"end":3070}},{"label":"td","span":{"begin":3071,"end":3075}},{"label":"td","span":{"begin":3076,"end":3080}},{"label":"td","span":{"begin":3081,"end":3088}},{"label":"tr","span":{"begin":3089,"end":3141}},{"label":"td","span":{"begin":3089,"end":3098}},{"label":"td","span":{"begin":3099,"end":3101}},{"label":"td","span":{"begin":3102,"end":3104}},{"label":"td","span":{"begin":3105,"end":3107}},{"label":"td","span":{"begin":3108,"end":3118}},{"label":"td","span":{"begin":3119,"end":3127}},{"label":"td","span":{"begin":3128,"end":3131}},{"label":"td","span":{"begin":3132,"end":3136}},{"label":"td","span":{"begin":3137,"end":3141}},{"label":"tr","span":{"begin":3142,"end":3200}},{"label":"td","span":{"begin":3142,"end":3153}},{"label":"td","span":{"begin":3154,"end":3157}},{"label":"td","span":{"begin":3158,"end":3160}},{"label":"td","span":{"begin":3161,"end":3163}},{"label":"td","span":{"begin":3164,"end":3174}},{"label":"td","span":{"begin":3175,"end":3183}},{"label":"td","span":{"begin":3184,"end":3188}},{"label":"td","span":{"begin":3189,"end":3193}},{"label":"td","span":{"begin":3194,"end":3200}},{"label":"tr","span":{"begin":3201,"end":3243}},{"label":"td","span":{"begin":3201,"end":3208}},{"label":"td","span":{"begin":3209,"end":3212}},{"label":"td","span":{"begin":3213,"end":3215}},{"label":"td","span":{"begin":3216,"end":3218}},{"label":"td","span":{"begin":3219,"end":3229}},{"label":"td","span":{"begin":3230,"end":3238}},{"label":"td","span":{"begin":3239,"end":3243}},{"label":"tr","span":{"begin":3244,"end":3251}},{"label":"td","span":{"begin":3244,"end":3251}},{"label":"tr","span":{"begin":3252,"end":3306}},{"label":"td","span":{"begin":3252,"end":3260}},{"label":"td","span":{"begin":3261,"end":3263}},{"label":"td","span":{"begin":3264,"end":3266}},{"label":"td","span":{"begin":3267,"end":3269}},{"label":"td","span":{"begin":3270,"end":3280}},{"label":"td","span":{"begin":3281,"end":3290}},{"label":"td","span":{"begin":3291,"end":3295}},{"label":"td","span":{"begin":3296,"end":3300}},{"label":"td","span":{"begin":3301,"end":3306}},{"label":"tr","span":{"begin":3307,"end":3363}},{"label":"td","span":{"begin":3307,"end":3316}},{"label":"td","span":{"begin":3317,"end":3319}},{"label":"td","span":{"begin":3320,"end":3322}},{"label":"td","span":{"begin":3323,"end":3325}},{"label":"td","span":{"begin":3326,"end":3336}},{"label":"td","span":{"begin":3337,"end":3347}},{"label":"td","span":{"begin":3348,"end":3352}},{"label":"td","span":{"begin":3353,"end":3358}},{"label":"td","span":{"begin":3359,"end":3363}},{"label":"tr","span":{"begin":3364,"end":3422}},{"label":"td","span":{"begin":3364,"end":3375}},{"label":"td","span":{"begin":3376,"end":3379}},{"label":"td","span":{"begin":3380,"end":3382}},{"label":"td","span":{"begin":3383,"end":3385}},{"label":"td","span":{"begin":3386,"end":3396}},{"label":"td","span":{"begin":3397,"end":3406}},{"label":"td","span":{"begin":3407,"end":3411}},{"label":"td","span":{"begin":3412,"end":3417}},{"label":"td","span":{"begin":3418,"end":3422}},{"label":"tr","span":{"begin":3423,"end":3465}},{"label":"td","span":{"begin":3423,"end":3430}},{"label":"td","span":{"begin":3431,"end":3434}},{"label":"td","span":{"begin":3435,"end":3437}},{"label":"td","span":{"begin":3438,"end":3440}},{"label":"td","span":{"begin":3441,"end":3450}},{"label":"td","span":{"begin":3451,"end":3460}},{"label":"td","span":{"begin":3461,"end":3465}},{"label":"table-wrap-foot","span":{"begin":3466,"end":3746}},{"label":"footnote","span":{"begin":3466,"end":3472}},{"label":"p","span":{"begin":3466,"end":3472}},{"label":"footnote","span":{"begin":3473,"end":3746}},{"label":"p","span":{"begin":3473,"end":3746}},{"label":"table-wrap-foot","span":{"begin":3747,"end":3778}},{"label":"footnote","span":{"begin":3747,"end":3778}},{"label":"label","span":{"begin":3747,"end":3748}},{"label":"p","span":{"begin":3749,"end":3778}},{"label":"table-wrap-foot","span":{"begin":3779,"end":3824}},{"label":"footnote","span":{"begin":3779,"end":3824}},{"label":"label","span":{"begin":3779,"end":3780}},{"label":"p","span":{"begin":3781,"end":3824}},{"label":"table-wrap-foot","span":{"begin":3825,"end":3871}},{"label":"footnote","span":{"begin":3825,"end":3871}},{"label":"label","span":{"begin":3825,"end":3826}},{"label":"p","span":{"begin":3827,"end":3871}},{"label":"table-wrap-foot","span":{"begin":3872,"end":3884}},{"label":"footnote","span":{"begin":3872,"end":3884}},{"label":"label","span":{"begin":3872,"end":3873}},{"label":"p","span":{"begin":3874,"end":3884}},{"label":"label","span":{"begin":3885,"end":3886}}],"tracks":[]}