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Diversity of lactase persistence in African milk drinkers.

Jones BL, Oljira T, Liebert A, Zmarz P, Montalva N, Tarekeyn A, Ekong R, Thomas MG, Bekele E, Bradman N, Swallow DM - Hum. Genet. (2015)

Bottom Line: Here we hypothesise that throughout Africa, where multiple functional alleles co-exist, the enhancer diversity will be greater in groups who are traditional milk drinkers than in non-milk drinkers, as the result of this sort of parallel selection.Amongst the Afro-Asiatic (Cushitic) language speaking Oromo, however, the geographic cline was not evident and the southern pastoralist Borana showed much higher LP frequency and enhancer diversity than the other groups.Together these results reflect the effects of parallel selection, the stochastic processes of the occurrence and spread of the mutations, and time depth of milk drinking tradition.

View Article: PubMed Central - PubMed

Affiliation: Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.

ABSTRACT
The genetic trait of lactase persistence is attributable to allelic variants in an enhancer region upstream of the lactase gene, LCT. To date, five different functional alleles, -13910*T, -13907*G, -13915*G, -14009*G and -14010*C, have been identified. The co-occurrence of several of these alleles in Ethiopian lactose digesters leads to a pattern of sequence diversity characteristic of a 'soft selective sweep'. Here we hypothesise that throughout Africa, where multiple functional alleles co-exist, the enhancer diversity will be greater in groups who are traditional milk drinkers than in non-milk drinkers, as the result of this sort of parallel selection. Samples from 23 distinct groups from 10 different countries were examined. Each group was classified 'Yes 'or 'No' for milk-drinking, and ethnicity, language spoken and geographic location were recorded. Predicted lactase persistence frequency and enhancer diversity were, as hypothesised, higher in the milk drinkers than the non-milk-drinkers, but this was almost entirely accounted for by the Afro-Asiatic language speaking peoples of east Africa. The other groups, including the 'Nilo-Saharan language speaking' milk-drinkers, show lower frequencies of LP and lower diversity, and there was a north-east to south-west decline in overall diversity. Amongst the Afro-Asiatic (Cushitic) language speaking Oromo, however, the geographic cline was not evident and the southern pastoralist Borana showed much higher LP frequency and enhancer diversity than the other groups. Together these results reflect the effects of parallel selection, the stochastic processes of the occurrence and spread of the mutations, and time depth of milk drinking tradition.

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Scatter plot showing correlation of nucleotide diversity (Pi) (Y axis) and inferred LP frequency (X axis) in different Oromo groups. This strong correlation r2 0.98 p ≪ 0.001 is attributable to co-selection of 5 different LP alleles. 4 newly collected, geographically distinct groups are shown as triangles, (see Supplementary Table 3 for data) in comparison with the Oromo collection shown in Table 1, (‘Oromo table 1’), and also the Oromo group previously published (Jones et al. 2013) (‘Various’), both of which are shown as squares. The data point marked as a darker triangle is that obtained from the pastoralist Borana from the south
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Fig4: Scatter plot showing correlation of nucleotide diversity (Pi) (Y axis) and inferred LP frequency (X axis) in different Oromo groups. This strong correlation r2 0.98 p ≪ 0.001 is attributable to co-selection of 5 different LP alleles. 4 newly collected, geographically distinct groups are shown as triangles, (see Supplementary Table 3 for data) in comparison with the Oromo collection shown in Table 1, (‘Oromo table 1’), and also the Oromo group previously published (Jones et al. 2013) (‘Various’), both of which are shown as squares. The data point marked as a darker triangle is that obtained from the pastoralist Borana from the south

Mentions: Since the difference in LP frequency and enhancer diversity in milk drinkers and non-milk drinkers is geographically structured, and is so confounded by difference in ancestry, we examined groups of more similar ethnic background, but whose lifestyle is different. We sequenced the enhancer region in 4 new groups of Oromo collected from distinct geographic regions (see Supplementary Table 1 and 3) that comprise one group of pastoralists, and 3 groups of agriculturalists who keep cows and drink milk. We compared these with the Oromo group described above and with the previously collected data from Oromo students, whose geographic origins were scattered (Jones et al. 2013). Again the LCT enhancer diversity is significantly correlated with inferred LP frequency r2 = 0.98 p ≪ 0.001 (Fig. 4), which is presumably attributable to the parallel selection of 5 different LP alleles in these related groups: the true pastoralists. The Borana, who are much more milk-dependent than the other groups, show by far the highest LP frequency and also LCT enhancer diversity. Notably, the same geographic cline in LCT diversity is not detected (Supplementary Table 1), with the most southerly group, the Borana, showing the highest diversity.Fig. 4


Diversity of lactase persistence in African milk drinkers.

Jones BL, Oljira T, Liebert A, Zmarz P, Montalva N, Tarekeyn A, Ekong R, Thomas MG, Bekele E, Bradman N, Swallow DM - Hum. Genet. (2015)

Scatter plot showing correlation of nucleotide diversity (Pi) (Y axis) and inferred LP frequency (X axis) in different Oromo groups. This strong correlation r2 0.98 p ≪ 0.001 is attributable to co-selection of 5 different LP alleles. 4 newly collected, geographically distinct groups are shown as triangles, (see Supplementary Table 3 for data) in comparison with the Oromo collection shown in Table 1, (‘Oromo table 1’), and also the Oromo group previously published (Jones et al. 2013) (‘Various’), both of which are shown as squares. The data point marked as a darker triangle is that obtained from the pastoralist Borana from the south
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4495257&req=5

Fig4: Scatter plot showing correlation of nucleotide diversity (Pi) (Y axis) and inferred LP frequency (X axis) in different Oromo groups. This strong correlation r2 0.98 p ≪ 0.001 is attributable to co-selection of 5 different LP alleles. 4 newly collected, geographically distinct groups are shown as triangles, (see Supplementary Table 3 for data) in comparison with the Oromo collection shown in Table 1, (‘Oromo table 1’), and also the Oromo group previously published (Jones et al. 2013) (‘Various’), both of which are shown as squares. The data point marked as a darker triangle is that obtained from the pastoralist Borana from the south
Mentions: Since the difference in LP frequency and enhancer diversity in milk drinkers and non-milk drinkers is geographically structured, and is so confounded by difference in ancestry, we examined groups of more similar ethnic background, but whose lifestyle is different. We sequenced the enhancer region in 4 new groups of Oromo collected from distinct geographic regions (see Supplementary Table 1 and 3) that comprise one group of pastoralists, and 3 groups of agriculturalists who keep cows and drink milk. We compared these with the Oromo group described above and with the previously collected data from Oromo students, whose geographic origins were scattered (Jones et al. 2013). Again the LCT enhancer diversity is significantly correlated with inferred LP frequency r2 = 0.98 p ≪ 0.001 (Fig. 4), which is presumably attributable to the parallel selection of 5 different LP alleles in these related groups: the true pastoralists. The Borana, who are much more milk-dependent than the other groups, show by far the highest LP frequency and also LCT enhancer diversity. Notably, the same geographic cline in LCT diversity is not detected (Supplementary Table 1), with the most southerly group, the Borana, showing the highest diversity.Fig. 4

Bottom Line: Here we hypothesise that throughout Africa, where multiple functional alleles co-exist, the enhancer diversity will be greater in groups who are traditional milk drinkers than in non-milk drinkers, as the result of this sort of parallel selection.Amongst the Afro-Asiatic (Cushitic) language speaking Oromo, however, the geographic cline was not evident and the southern pastoralist Borana showed much higher LP frequency and enhancer diversity than the other groups.Together these results reflect the effects of parallel selection, the stochastic processes of the occurrence and spread of the mutations, and time depth of milk drinking tradition.

View Article: PubMed Central - PubMed

Affiliation: Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.

ABSTRACT
The genetic trait of lactase persistence is attributable to allelic variants in an enhancer region upstream of the lactase gene, LCT. To date, five different functional alleles, -13910*T, -13907*G, -13915*G, -14009*G and -14010*C, have been identified. The co-occurrence of several of these alleles in Ethiopian lactose digesters leads to a pattern of sequence diversity characteristic of a 'soft selective sweep'. Here we hypothesise that throughout Africa, where multiple functional alleles co-exist, the enhancer diversity will be greater in groups who are traditional milk drinkers than in non-milk drinkers, as the result of this sort of parallel selection. Samples from 23 distinct groups from 10 different countries were examined. Each group was classified 'Yes 'or 'No' for milk-drinking, and ethnicity, language spoken and geographic location were recorded. Predicted lactase persistence frequency and enhancer diversity were, as hypothesised, higher in the milk drinkers than the non-milk-drinkers, but this was almost entirely accounted for by the Afro-Asiatic language speaking peoples of east Africa. The other groups, including the 'Nilo-Saharan language speaking' milk-drinkers, show lower frequencies of LP and lower diversity, and there was a north-east to south-west decline in overall diversity. Amongst the Afro-Asiatic (Cushitic) language speaking Oromo, however, the geographic cline was not evident and the southern pastoralist Borana showed much higher LP frequency and enhancer diversity than the other groups. Together these results reflect the effects of parallel selection, the stochastic processes of the occurrence and spread of the mutations, and time depth of milk drinking tradition.

Show MeSH
Related in: MedlinePlus