X‐chromosomal genetic diversity and linkage disequilibrium patterns in Amerindians and non‐Amerindian populations

Abstract

In accordance to previous work done with other populations, human isolates, such as Amerindian tribes, seem to be an optimal choice for the implementation of association studies due to the wide extent of LD which can be found in their gene pool. On the other hand, the low proportion of loci in LD found in both admixed populations studied here could be explained by events related to their history and similarities between the allele frequencies in the parental stocks.

Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample

“…In the sample investigated, we did not find any evidence of linkage disequilibrium between close or linked markers. LD does not only depend on the physical distance between loci and may result from the breeding system, the pattern of geographic subdivision, gene flow, genetic drift, mutation and other forces that cause gene-frequency evolution [23,24]. Nevertheless, the three significant results obtained are probably a consequence of sampling effects since these associations were not observed in the studies conducted so far.…”

High‐resolution HLA allele and haplotype frequencies in majority and minority populations of Costa Rica and Nicaragua: Differential admixture proportions in neighboring countries

“…A summary on sample size, number of alleles per locus, heterozygosity, adherence to HWE, and neutrality tests in all populations is presented in Table 1. An average of 32 (range 24-37), 51 (34-64), 25 (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30), and 35 (26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40) alleles were identified for HLA-A, -B, -C, and -DRB1 in each of the five populations, respectively. Of note, the lowest number of alleles for each locus was found in the sample of CRAI.…”

“…Regional genetic variation in Costa Rica has already been suggested by other genetic markers. [14][15][16][17] Moreover, the major population of Costa Rica, that of its Central Valley, has been the subject of genetic scientific interest [18][19][20][21][22][23][24][25][26] due to its interesting demographic history including claims for relative isolation, 27,28 while that of its northwestern province of Guanacaste has been a hub for largescale human papilloma virus vaccine testing clinical trials. [29][30][31][32][33] All these characteristics make the study of HLA allele and haplotype frequencies in these countries of special interest.…”

Brazilian quilombos: A repository of Amerindian alleles

“…For example, reductions in effective population size could cause decreased recombination and consequent LD. Furthermore, isolation is another aspect to be considered, as many examples of low genetic diversity and high LD have been described (Laan and P€ a€ abo, 1997;Varilo et al, 2000;Katoh et al, 2002;Amorim et al, 2011b). In this scenario, one would expect to find LD in small and isolated populations such as STI and especially SAG, which is smaller and more isolated.…”

“…LD can therefore indicate past demographic events such as expansions and retractions in population effective size, the existence of population structure, and admixture Slatkin, 2008;Amorim et al, 2011b). For example, reductions in effective population size could cause decreased recombination and consequent LD.…”