Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.

非洲比任何其他大洲都拥有更多的人类遗传变异，但是对非洲人民的大多数人口规模分析都只关注四个主要语言群体中的两个，即尼日尔-刚果和非裔亚洲人，而尼罗-撒哈拉以南和科伊桑人的人数不足。为了评估Nilo-Saharan种群内以及Nilo-Saharan与Niger-刚果和非裔亚洲人之间的遗传变异和选择标记，我们对乌干达西北的Nilo-Saharan Lugbara种群的50个基因组和250个基因组进行了测序来自6个先前未排序的尼日尔-刚果人口。我们将这些数据与来自其他16个欧亚和非洲人口的数据进行了比较，其中包括古穆兹（Gumuz），这是埃塞俄比亚的另一个推定的尼罗-撒哈拉人口。在Nilo-Saharan人口中发现的2100万变体中，有3。dbSNP中未显示5700万（17％），其中包括预测的可能具有表型效应的非同义突变。我们发现，尼罗撒哈拉沙漠卢格巴拉族和古穆兹族之间的遗传分化比任何两个亚非或尼日尔-刚果族之间更大。F3测试表明，古木兹（Gumuz）为大多数尼日尔-刚果B人口贡献了遗传成分，而卢加巴拉（Lugabara）没有。我们扫描了Lugbara的基因组以寻找选择性扫描的证据。我们在四个位点（F3测试表明，古木兹（Gumuz）为大多数尼日尔-刚果B人口贡献了遗传成分，而卢加巴拉（Lugabara）没有。我们扫描了Lugbara的基因组以寻找选择性扫描的证据。我们在四个位点（F3测试表明，古木兹（Gumuz）为大多数尼日尔-刚果B人口贡献了遗传成分，而卢加巴拉（Lugabara）没有。我们扫描了Lugbara的基因组以寻找选择性扫描的证据。我们在四个位点（与皮肤色素沉着相关的SLC24A5，SNX13，TYRP1和UVRAG），据报道其中三项已在选择中。这些选择性扫描指向适应萨赫勒地区强烈的紫外线辐射。