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
Affiliations
Tom van der Valk
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Corresponding author
Marianne Dehasque
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
J. Camilo Chacón-Duque
Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, SE-1069, Stockholm, Sweden
Nikolay Oskolkov
Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Sweden
Sergey Vartanyan
North-East Interdisciplinary Scientific Research Institute n.a. N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan, Russia
Peter D. Heintzman
The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
Patrícia Pečnerová
Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
David Díez-del-Molino
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
Love Dalén
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden; Corresponding author
Summary: 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.
