Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome

Tom van der Valk; Marianne Dehasque; J Camilo Chacón-Duque; Nikolay Oskolkov; Sergey Vartanyan; Peter D Heintzman; Patrícia Pečnerová; David Díez-Del-Molino; Love Dalén

doi:10.1016/j.isci.2022.104826

Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome

iScience. 2022 Aug 1;25(8):104826. doi: 10.1016/j.isci.2022.104826. eCollection 2022 Aug 19.

Authors

Tom van der Valk^{1

2}, Marianne Dehasque^{1

2

3}, J Camilo Chacón-Duque^{2

4}, Nikolay Oskolkov⁵, Sergey Vartanyan⁶, Peter D Heintzman⁷, Patrícia Pečnerová⁸, David Díez-Del-Molino^{1

2

3}, Love Dalén^{1

2

3}

Affiliations

¹ Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
² Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden.
³ Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden.
⁴ Department of Archaeology and Classical Studies, Stockholm University, SE-1069, Stockholm, Sweden.
⁵ Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Sweden.
⁶ North-East Interdisciplinary Scientific Research Institute n.a. N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan, Russia.
⁷ The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway.
⁸ Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

Abstract

Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In this study, we sequenced two woolly mammoth genomes and combined these with previously sequenced mammoth and elephant genomes to conduct a survey of mammoth-specific deletions and indels. We find that deletions are highly enriched in non-coding regions, suggesting selection against structural variants that affect protein sequences. Nonetheless, at least 87 woolly mammoth genes contain deletions or indels that modify the coding sequence, including genes involved in skeletal morphology and hair growth. These results suggest that deletions and indels contributed to the unique phenotypic adaptations of the woolly mammoth, and were potentially critical to surviving in its natural environment.

Keywords: Bioinformatics; Biological sciences; Evolutionary biology; Natural sciences; Phylogenetics; Zoology.