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Thread: Genomic selection in Nilo-Saharan and Niger-Congo speakers (Pre-print)

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    Genomic selection in Nilo-Saharan and Niger-Congo speakers (Pre-print)

    Pre-print: Genomic evidence for population specific selection in Nilo-Saharan and Niger-Congo linguistic groups in Africa

    Abstract:
    Background: There are over 2000 genetically diverse ethnolinguistic groups in Africa that could help decipher human evolutionary history and the genetic basis of phenotypic variation. We have analysed 298 genomes from Niger Congo populations from six sub Saharan African countries (Uganda, Democratic Republic of Congo, Cameroon, Zambia, Ivory Coast, Guinea) and a Nilo Saharan population from Uganda. These samples were collected as part of the TrypanoGEN consortium project http://www.trypanogen.net. Results: The population genetic structure of the 298 individuals revealed four clusters which correlated with ethnolinguistic group and geographical latitude, that is, West African Niger-Congo A, Central African Niger Congo, East African Niger-Congo B and the NiloSaharan. We observed a spatial distribution of positive natural selection signatures in genes associated with AIDS, Tuberculosis, Malaria and Human African Trypanosomiasis among the TrypanoGEN samples. Having observed a marked difference between the NiloSaharan Lugbara and Niger Congo populations, we identified four genes [APOBEC3G, TOP2B, CAPN9, LANCL2, (iHS -log p > 3.0, Rsb -log p > 3.0, Fst > 0.1 Bonferroni p > 1.8x10e4)], which are highly differentiated between the two ethnic groups and under positive selection in the Lugbara population. Conclusion: The signatures that differentiate ethnically distinct populations provide information on the specific ecological adaptations with respect to disease history and susceptibility/ resistance; as demonstrated in this study where APOBEG3G is believed to be involved in the susceptibility of the Nilo Saharan Lugbara population to Hepatitis B virus infection.
    This is more of a medical genetics paper but they did do a ADMIXTURE run and some dating work.

    They refer to the Lugbara as Nilotic here but they're normally classed as Central Sudanic:
    Ugandan Bantu and Ugandan Nilotic appeared to begin separating from other populations about 23 and 47kya, respectively and became isolated about 3kya but these estimations may be confounded by admixture.
    At K=6 The Niger-Congo populations exhibited 17-60% 122 admixture with minor ancestries, whilst the Ugandan Nilo-Saharan population had 7% admixture with Niger Congo ancestries
    ADMIXTURE:
    admixture.png
    Last edited by blackflash16; 09-11-2017 at 12:01 AM.

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