Abstract
BackgroundInferring history from genomic sequences is challenging and problematic because chromosomes are mosaics of thousands of small Identicalby-descent (IBD) fragments, each of them having their own unique story. However, the main events in recent evolution might be deciphered from comparative analysis of numerous loci. A paradox of why humans, whose effective population size is only 104, have nearly three million frequent SNPs is formulated and examined.ResultsWe studied 5398 loci evenly covering all human autosomes. Common haplotypes built from frequent SNPs that are present in people from various populations have been examined. We demonstrated highly non-random arrangement of alleles in common haplotypes. Abundance of mutually exclusive pairs of common haplotypes that have different alleles at every polymorphic position (so-called Yin/Yang haplotypes) was found in 56% of loci. A novel widely spread category of common haplotypes named Mosaic has been described. Mosaic consists of numerous pieces of Yin/Yang haplotypes and represents an ancestral stage of one of them. Scenarios of possible appearance of large number of frequent human SNPs and their habitual arrangement in Yin/Yang common haplotypes have been evaluated with an advanced genomic simulation algorithm.ConclusionsComputer modeling demonstrated that the observed arrangement of 2.9 million frequent SNPs could not originate from a sole stand-alone population. A “Great Admixture” event has been proposed that can explain peculiarities with frequent SNP distributions. This Great Admixture presumably occurred 100–300 thousand years ago between two ancestral populations that had been separated from each other about a million years ago. Our programs and algorithms can be applied to other species to perform evolutionary and comparative genomics.
Highlights
Inferring history from genomic sequences is challenging and problematic because chromosomes are mosaics of thousands of small Identicalby-descent (IBD) fragments, each of them having their own unique story
By analyzing common haplotypes in 62 random genomic loci and 85 gene-coding regions in humans, the Zhang et al study proposed that the Yin/Yang haplotypes are abundant throughout the human genome and are genetic signatures that emerged prior to the African diaspora
We studied haplotypes built from 50 adjacent Genetic variants (GV) occurring with high frequency in modern humans (which Minor Allele Frequency (MAF) was >25% among 1092 sequenced genomes)
Summary
Inferring history from genomic sequences is challenging and problematic because chromosomes are mosaics of thousands of small Identicalby-descent (IBD) fragments, each of them having their own unique story. Our team computationally processed this database and demonstrated that very rare genetic variants (vrGVs, whose frequencies are less than 0.2%) are valuable markers for deciphering distant human relatedness [8, 9] This examination brought to light the human migration routes and admixture that happened up to ten thousand years ago. To reveal more distant events in the history of mankind, genetic variants (GVs) with higher frequencies should be assessed Keeping this in mind, here we investigated the distribution and structure of haplotypes built from the most frequent GVs (whose minor allele frequencies (MAF) are >25%) in people from Africa, America, Asia, and Europe (>90% of these GVs are SNPs). The Mosaic haplotypes are built from multiple small pieces of Yin/Yang haplotypes
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