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Human Deletion Variants that are Shared with the Genomes of Archaic Hominins – Evolution and Functional Impact

Various interpretations of allele sharing between modern and archaic genomes have been proposed as having originated from ancestral genetic structure or from archaic hominins through introgression from non-Africans. However the evolution of polymorphic human deletions has not yet been studied. Lin et al. have identified 427 polymorphic human deletions that are shared with the genomes of archaic hominins, of which about 87 % originated prior to Neanderthal-Human divergence (ancient) and only about 9 % of which have been introgressed from Neanderthals. The remaining about 4 % of allele sharing between humans and archaic hominins is constituted of the recurrence, lineage sorting that is incomplete between lineages of humans and chimps, and human-specific insertions. Lin et al. observed that among modern humans ancient deletions correspond to more than 13 % of all common (>5 % allele frequency) deletion variation. It is indicated by their analysis that ancient and introgressed deletion variants the genomic landscapes were primarily shaped by purifying selection, which eliminated large and exonic variants. The results of this analysis showed that 17 exonic deletions had been found that are shared with archaic hominin genomes, including those which led to 3 fusion transcripts. The affected genes were involved in metabolism and external and internal compounds, growth and the formation of sperm, as well as the susceptibility to psoriasis and Crohn’s disease. Also, this analysis suggests these “exonic” deletion variants evolved through different adaptive forces, which included balancing and population-specific positive selection. It is revealed by the findings of this study that genomic structural variants shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionary important phenotypes.


Deletion variants, the best characterised of all genomic structural variants, have been shown to have played an important role in the evolution of humans (McLean et al., 2011). However, it has not been well established what the evolutionary role of these variants is within species. Study of human deletion variation in a population genetics framework has recently been allowed by high-quality sequences and, more importantly, highly improved discovery and genotyping tools that were primarily developed within the context of the 1000 Genomes Project. These resources were used by Lin et al. to assess deletion variants in humans that they share with Neanderthal and Denisovan genomes. This allowed them to:

  • Identify hundreds of ancient and introgressed deletion variants in humans;

  • Investigate deletion variation in haplotypic backgrounds;

  • Shed light on individual deletion variants that may have phenotypic effects.

Lin et al., believe this is the first study in which deletion variation was documented and characterised in humans that are shared with the genomes of Neanderthals and Denisovans in a genome-wide context.

The majority of allele sharing that involves deletion variants between modern humans and archaic hominins is suggested by the results of this study to be due to ancestral structure and not due to introgression. Also, according to Lin et al. this observation highlights a largely unexplored deep ancestry for a considerable part, about 13 %, of common deletion variants in humans, and does not conflict with recent reports regarding introgression for Neanderthals and Denisovans to modern humans. Also, the genomic distribution of these variants shows signatures of ancient purifying selection, which results in only a few exonic variants not being elimination. Similar observations that have been made for deletions in general have been complemented by this observation (Mills et al., 2011), further suggesting the potential role for recent, rare deletion variants in detrimental phenotypes and disease (Itsara et al., 2009).

Of these ancient and introgressed deletions only a very low percentage, about 4 %, that have been maintained are exonic; though the genes involved affect phenotypes that are evolutionarily relevant, such as growth, immunity and metabolism of external and internal compounds. Common diseases in humans, such as Crohn’s disease and psoriasis, are also associated with these deletions. Lin et al. say Exonic deletions are functionally drastic events that are comparable to frame-shift, or mutations that introduce a stop-codon, or to multiple nonsynonymous single nucleotide variants if the gene continues to function. As such, Lin et al. argue that deletions that overlap with exons that have been maintained since the divergence of humans from Neanderthals are not likely to have evolved under natural conditions, which isn’t the case with the majority of ancient deletions. Instead, these exons may have been maintained by a combination of:

·         Adaptive forces that are geographically different, potentially are frequency-dependent,

·         Balancing selection.

They argue that pathways involving these important phenotypes are viable targets for some form of complex adaptive selection that aided in maintaining the genetic structural variation at these loci over a period of hundreds of thousands of years.

Sources & Further reading

  1. Lin, Y.-L., P. Pavlidis, E. Karakoc, J. Ajay and O. Gokcumen (2015). "The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes." Molecular Biology and Evolution 32(4): 1008-1019.


Author: M. H. Monroe
Last Updated 18/03/2016
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