Francis-Guiblet, Wilfried M.

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    Signatures of selection in the indel-containing coding sequences from human to primate genome comparisons
    (2013) Francis-Guiblet, Wilfried M.; Oleksyk, Taras K.; College of Arts and Sciences - Sciences; Martínez Cruzado, Juan C.; Ríos Velázquez, Carlos; Massey, Steven E.; Department of Biology; Ortíz, Juan A.
    Gene sequences are relatively conserved, and usually show few differences in comparisons between closely related species, such as between humans and non- human primates. In this study, we focused on >10 bp insertions and deletions (Indels) found in the alignments between the human, chimpanzee, gorilla, orangutan, and rhesus macaque reference genome sequences and examined these regions in order to characterize signatures of adaptive and non-adaptive evolution in the phylogenetic lineage leading to our own species. A public data set of 36,422 Indels identified by comparing the reference genomes was filtered to set aside 146 Indels within coding sequences (with a potentially high impact on proteins). Among these, 80 fragments were successfully amplified by PCR and visualized on electrophoresis gels to distinguish real features from the computational artifacts. Only 22 Indels could be related to specific feature in the sequence alignment using the reference genomes. These Indel-containing genes were interrogated for the signatures of selection with PAML package by producing pairwise Ka/Ks ratios in all species comparisons. The significance of this approach was evaluated by a resampling method, where exactly the same procedures and tests were performed with a dataset of randomly created Indels (simdels) matched by size and distributed across the reference genomes. Indels showed significantly higher Ka/Ks ratios indicating that they were located in less constrained sequences, and a trend was observed with first exons showing the largest difference between the observed Indels and simdels. We also searched for more recent signatures of selection by searching for the chromosomal regions demonstrating diminished multilocus heterozygosity and high population divergence (FST) by comparing dense genotyping data in the moving windows along the chromosomes between populations of the Human Genome Diversity Project (HGDP). We identified several genes by comparing the observed distribution to a distribution of simdels and discussed our results in from the prospective of relevant evolutionary history during major human migrations.