Short tandem repeat polymorphism evolution in humans

Abstract

Forty-five dinucleotide short tandem repeat polymorphisms were typed in ten large samples of a globally distributed set of populations. Although these markers had been selected for high heterozygosity in European populations, we found them to be sufficiently informative for linkage analysis in nonEuropeans. Heterozygosity, mean number of alleles, and mean number of private alleles followed a common trend: they were highest in the African samples, were somewhat lower in Europeans and East Asians, and were lowest in Amerindians. Genetic distances also reflected this pattern, and distances modelled after the stepwise mutation model yielded trees that were less in agreement with other genetic and archaeological evidence than distances based on differentiation by drift (F ST ). Genetic variation in nonAfricans seems to be a subset of that in Africans, supporting the replacement hypothesis for the origin of modern humans.

An evolutionary approach to the medical implications of the tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) gene

“…In contrast with the trend observed for several other genes, [18][19][20] this sample displayed one of the lowest values of nucleotide diversity, as well as a lower value of haplotype diversity with respect to North African and Middle Eastern samples. Usually a lower level of genetic diversity is found in non-African populations and it is universally accounted as a consequence of the strong bottleneck experienced by the groups of modern humans that migrated out of Africa, starting from 100 000 to 50 000 years ago.…”

“…edu/) and also higher than the value obtained as an average for 8 genes from the Innate Immunity Program in Genomics Application database (p ¼ 0.00094) (http:// innateimmunity.net/), recently surveyed for signatures of selection. 17 The sub-Saharan African sample showed one of the lowest values of nucleotide diversity (p ¼ 0.00063), in contrast with the trend observed for several other genes, [18][19][20] but see Mateu et al 21 for a counterexample, and for Seattle SNPs resequenced genes, for which African Americans showed greater nucleotide diversity than European Americans in 82.6% of the cases.…”

“…16,23 This was also confirmed by the observed linkage disequilibrium (LD) patterns, which were characterized by low average r 2 values for all SNPs pair-wise comparisons (ZnS), with values ranging from ZnS ¼ 0.06 for the central Asian sample to ZnS ¼ 0.12 for the Val di Scalve sample. This pointed out an overall picture of low LD for the TNFRSF13B region, in which Italian, Middle Eastern and North African healthy samples showed the highest percentages of significant SNPs pair-wise comparisons (19,13 and 12%, respectively). Very similar D 0 /LOD plots, with the same small LD block, were indeed obtained for Middle Eastern, North African and CVID samples, whereas Italian and IgAD groups showed a greater LD block, which was reduced in the Val di Scalve population because of the The five most frequent inferred haplotypes accounted for 68% of sampled chromosomes ( Figure 2).…”

Genetic variation, classification and 'race'

“…This allows us to 'root' the tree and shows that the root falls closest to African populations. All of these findings, which are in accord with many other studies based on different types of genetic variation assessed in different samples of humans [25][26][27][28] , support an evolutionary scenario in which anatomically modern humans evolved first in Africa, accumulating genetic diversity. A small subset of the African population then left the continent, probably experienced a population bottleneck and founded anatomically modern human populations in the rest of the world 29 .…”

Association study using combination analysis of SNP and STRP markers: CD14 promoter polymorphism and IgE level in Taiwanese asthma children

“…Another important issue is the degree to which populations differ in terms of genetic susceptibility and linkage disequilibrium (LD) structure and therefore the need to sample from different population groups in disease studies. Owing to historical isolation, major racial/ethnic groups differ in allele frequencies (Stephens et al 2001;Calafell et al 1998). These differences are highly significant, especially for less common alleles; often, a particular allele was found in one population at modest frequency and missing from others (Stephens et al 2001).…”