Ancestral Genomes and the History of Adaptation

Ancestral Genomes and the History of Adaptation

Ancestral Genomes and the History of Adaptation

Maha M Osman1, 2, Rayan S Ali1, Mahmoud Koko1, Muntaser E Ibrahim1*

1 Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.

2 Commission for Biotechnology and Genetic Engineering, National Center for Research, Sudan.

*Corresponding author: Prof. Muntaser E Ibrahim, mibrahim@iend.org

Abstract

The evolutionary history of a species is best seen from the summation of genetic variation across its genome. Genomes of African populations are believed to have retained some of the ancestral states of their genetic variation based on autosomes and sex specific chromosomes as well. In order to understand the evolutionary history of human populations in relation to other hominines, including the Neanderthal as a close species, and in attempt to gain insights to mechanisms of human adaptation, genomic data in different classes of adaptive traits were compared. Sudanese samples were sequenced on IlluminaHiSeq2000 platform. Sequences were compared to Neanderthal and global samples collected from 1000 Genomes and UCSC browsers.  Genes of adaptive traits and whole mitochondrial genomes and genes were extracted using Linux commands and Bioinformatics tools. Different software programs and statistical methods were used include; population differentiation test (FST), principal component analyses (PCA), Tajima Test for selective neutrality, phylogenetic trees were constructed using BEAST and MEGA7. Whole mitogenomes produced robust phylogenies that were greatly concordant with available HVRI, indicating that the HVRI has the upper hand in depicting the overall information content of the mtDNA sequence variation. Skyline plots based on HVRI show expansion dates to alter when the north eastern sequences are used compared to the plot of the world population, indicating the pivotal contribution of east Africans to human key evolutionary events. The results indicate that although Neanderthal and humans are adequately divergent in terms of speciation and genetic distance, ample variations are retained more pronouncedly in the biological class of variations.  Interestingly and as manifestation of the peculiarity of cultural variations to humans there was an observed divergence between humans and Neanderthal, manifested in reduced clustering and higher distance metrics, indicating the effect of cultural evolutionary forces.

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