Woolly mammoths had a set of unique adaptations that enabled them to thrive in the extreme Arctic environment. To date, a large set of mammoth-specific, protein-changing single nucleotide polymorphisms (SNPs) have been identified using ancient genomes. Although these SNPs are responsible for many mammoth traits, a multitude of other genetic variants likely contributed to the evolution of the woolly mammoth. In this study we sequenced two woolly mammoth genomes to high coverage and combined these with published high-coverage mammoth and elephant genomes to conduct a broad survey of mammoth-specific large deletions and shorter insertions and deletions. We find that deletions and indels are highly enriched in non-coding regions, suggesting strong selection against structural variants that affect protein sequences. Nonetheless, we find that at least 87 woolly mammoth genes are affected by deletions or indels in the mammoth lineage, including genes involved in skeletal morphology, body size, hair growth, body-fat distribution and behaviour. These results suggest that deletions and indels likely had an important role in the unique phenotypic adaptations of the woolly mammoth, and thus, need to be considered for de-extinction of this species through genetic engineering.
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