Linkage disequilibrium patterns and genetic structure of Amerindian and non‐Amerindian Brazilian populations revealed by long‐range X‐STR markers

Abstract

The extent of X-chromosome linkage disequilibrium (LD) was studied in a southern Brazilian population, and in a pool of samples from Amerindian populations. For this purpose, 11 microsatellites, located mostly in a Xq region comprising approximately 86 Mb was investigated. The lower Amerindian gene diversity associated with significant differences between the populations studied indicated population structure as the main cause for the higher LD values in the Amerindian pool. On the other hand, the LD levels of the non-Amerindian Brazilian sample, although less extensive than that of the Amerindians, were probably determined by admixture events. Our results indicated that different demographic histories have significant effects on LD levels of human populations, and provide a first approach to the X-chromosome ancestry of Amerindian and non-Amerindian Brazilian populations, being valuable for future studies involving mapping and population genetic studies.

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

“…Thus, the lower genetic diversity and the higher level of LD observed in the Native populations, as compared to the CVCR and Gaucho samples, might be associated with these phenomena. Similar results were obtained in previous independent studies involving South Amerindian (Leite et al, 2009;Wang et al, 2010) and other small and isolated populations such as the Khoton from Mongolia (Katoh et al, 2002), the Saami (Laan and Pä ä bo, 1997), and Kuusamo (Varilo et al, 2000) from Finland.…”

“…This work shows some similarities to ours, with lower locus diversity, lower number of alleles per site, and higher LD among Amerindians as compared to the admixed populations. The diversity indices, however, are slightly lower in our work, indicating that the set of markers used by Leite et al (2009) is more variable than ours, which may also be linked to the wider extent of LD detected in our study. Mention should also be made of the differences between the correction procedures and methods for LD detection used in both studies, which may have influenced the LD comparison.…”

“…The comparison between X-chromosomal diversity and LD between Amerindian and admixed groups was already examined in a previous investigation (Leite et al, 2009). This work shows some similarities to ours, with lower locus diversity, lower number of alleles per site, and higher LD among Amerindians as compared to the admixed populations.…”

“…Notwithstanding linkage disequilibrium investigations among them are scarce. We therefore developed an investigation design, which is an extension of previous and recent investigations on X-STR LD in distinct pools of Amerindian and non-Amerindian samples (Leite et al, 2009;Wang et al, 2010). In our study three relatively isolated Native American populations and two non-native communities were tested for a fast-evolving genetic system, with the following questions in mind: (a) since genetic variability clearly influences the power to detect LD, do the populations investigated here show differences in this characteristic that could influence the patterns obtained?…”

Aplicabilidade do cromossomo X no DNA forense

“…O polimorfismo presente nesse cromossomo vem atraindo cada dia mais a atenção de pesquisadores. Inúmeros estudos na população brasileira demonstraram que vários marcadores moleculares situados no cromossomo X já são validados para uso forense, sendo que estes apresentam resposta no que tange sobre a variabilidade desses polimorfismos na população (CAINÉ et al, 2007;CAINÉ et al, 2010;GUSMÃO et al, 2009;LEITE et al, 2009;MARTINS et al, 2008a;MARTINS et al, 2009;MARTINS et al, 2010a;MARTINS et al, 2010b;PENNA et al, 2011;RODRIGUES et al, 2010;RODRIGUES et al, 2011;SILVA et al, 2010;TAVARES et al, 2008). Na rotina forense, os marcadores do tipo STR mais utilizados são os localizados nos cromossomos autossômicos e no Y (TOMAS et al, 2015).…”