Y-specific restriction fragment length polymorphisms In Southern African populations.
Date
1992
Authors
Spurdle, Amanda B
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Abstract
Seven Y chromosome probes and thirteen restriction enzyme digests were used to examine a conservative estimate of 20000bp, and no new Y-specific polymorphisms were revealed by these systems. The Y chromosome probe 49a, which reveals a Y-specific haplotype with TaqI, was shown to reveal five new complex polymorphisms with Bglll, Hindlll, Pst I, PvuII and Sstl. The new polymorphisms exhibit great genetic diversity, and each enzyme reveals numerous haplotypes, which mostly occur infrequently and are population-specific. The haplotypes for a given enzyme do not correlate strictly with those revealed by the other enzymes, including TaqI, suggesting that each polymorphism results from a combination of restriction site mutations and rearrangement events. Association between the different 49a polymorphisms occurs only in individuals of recent common genetic origin.
Y-specific 49a/TagI haplotypes were determined for 933 individuals drawn from 23 different African populations. A total of 31 new haplotypes were observed, some of which contained new alleles or allelic variants. Duplication, in addition to CpG mutation, is implicated in the generation of certain allelic variants. Cluster analysis of genetic distances
between populations was calculated using the 49a/TagI haplotype frequencies. Y-specific 49a/TagI haplotype analysis of individual populations was not sufficiently sensitive to accurately distinguish between the different Bantu-speaking Negroid tribal groups. Cluster analysis of larger groupings was more stable, and with the exception of the Khoisan, resulted in a basic split between African and non-African populations.
The linkage disequilibrium of the XY275 MspI Y-linked polymorphism was determined. The high allele was generally found in association with the Y chromosome, but the Y-associated low allele was found to occur in Bantu-speaking Negroids, Khoisan-speaking Negroids, the Khoisan, two groups of mixed ancestry, and the Caucasoid South African Asiatic Indian population. The discovery of Y-associated low alleles in non-African as well as African populations suggests that more than one Y chromosome gave rise to the present-day non-African population.
The pDP31/EcoRI, p21Al/TagI and Y Alu polymorphisms were also studied in several southern African populations. The pDP31 duplication occurred at high frequencies in Caucasoids, and could be used to indicate Caucasoid male gene flow into hybrid populations. The p21Al/TagI point mutation showed no
distinct trends in frequency in the different populations, and several Taql mutations are proposed to have occurred in the repeat unit recognized by this sequence. The Y Alu polymorphism occurred infrequently in Caucasoids, at intermediate frequency in the Khoisan, and at high frequency in Negroids. The presence of the Y Alu insertion in all three major population groups studied is interpreted to suggest that the insert predates the diversification of Homo sapiens.
The relationship between the different Y-linked polymorphisms was determined in the populations studied. The Y Alu polymorphism is believed to have originated once from sequencing data, but such information is not available for the other Y polymorphisms studied. No absolute relationship was observed between the Y Alu polymorphism and the 49a/TagI, XY275 Mspl, pDP31/£coRI and p21Al/TagI polymorphisms. It is suggested that the latter polymorphisms have arisen more than once.
Description
A thesis submitted to the Faculty of Medicine University of the Witwatersrand, Johannesburg fulfilment of the requirements for the degree of Philosophy