Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic

Vincent J. Lynch, Oscar C. Bedoya-Reina, Aakrosh Ratan, Michael Sulak, Daniela I. Drautz-Moses, George H. Perry, Webb Miller, Stephan C. Schuster
2015 Cell Reports  
Woolly mammoths and the living elephants are characterized by major phenotypic differences that allowed them to live in very different environments. To identify the genetic changes that underlie the suite of adaptations in woolly mammoths to life in extreme cold, we sequenced the nuclear genome from three Asian elephants and two woolly mammoths, identified and functionally annotated genetic changes unique to the woolly mammoth lineage. We find that genes with mammoth specific amino acid changes
more » ... amino acid changes are enriched in functions related to circadian biology, skin and hair development and physiology, lipid metabolism, adipose development and physiology, and temperature sensation. Finally we resurrect and functionally test the mammoth and ancestral elephant TRPV3 gene, which encodes a temperature sensitive transient receptor potential (thermoTRP) channel involved in thermal sensation and hair growth, and show that a single mammoth-specific amino acid substitution in an otherwise highly conserved region of the TRPV3 channel strongly affected its temperature sensitivity. Our results have identified a set of genetic changes that likely played important roles in the adaptation of woolly mammoths to life in the high artic. peer-reviewed) adaptations to the artic are almost entirely unknown. Whole-genome sequencing (WGS) is an invaluable tool for exploring the genetic origins of phenotypic differences between species because one can identify fixed and polymorphic variants across the genome without respect to a priori defined genes and pathways. However, distinguishing functional from nonfunctional variants in WGS data can be difficult (Cooper and Shendure, 2011) . To determine genetic changes that underlie cold-adapted traits in woolly mammoths we sequenced the genomes of three Asian elephants and two woolly mammoths to high coverage, and functionally annotated fixed, derived amino acid and loss of function substitutions in woolly mammoths. We found that genes with woolly mammoth-specific substitutions were enriched in functions related to circadian biology, skin, hair, and sebaceous gland development and physiology, lipid metabolism, adipose development and physiology, and temperature sensation. We experimentally validated a fixed woolly mammoth-specific hypomorphic substitution in the temperature sensor TRPV3 that we predict influenced both thermal sensation and hair growth in mammoths. These data provide mechanistic insights into the causes of morphological evolution, and define a set of likely casual variants for future study of woolly mammoth-specific traits. RESULTS AND DISCUSSION Genome sequencing, assembly, and annotation We generated Illumina sequence data for two woolly mammoths that died ~20,000 and ~60,000 years ago (Gilbert et al., 2008; 2007; Miller et al., 2008) , including individuals from the two major lineages of woolly mammoths, clade I (individual M4) and clade II (M25), which diverged ~1.5 MYA (Miller et al., 2008) , and three extant Asian elephants (Elephas maximus). We aligned sequencing reads to the genome assembly for the African Savannah elephant (Loxodonta africana), resulting in non-redundant average sequence coverage of ~20-fold for each mammoth and ~30-fold for each Asian elephant (SI Fig. 1) . We identified ~33 million putative single-nucleotide variants (SNVs) among the three elephantid species (see Methods for details), including ~1.4 million nucleotide variants fixed for the derived allele in the two mammoths, but for the ancestral allele in the African and Asian elephants. Among the variants were 2,020 mammoth-specific amino-acid substitutions in a total of 1,642 protein-coding genes, including 26 protein-coding genes with premature stop codons (putative loss of function substitutions). We also identified a single gene with a strongly peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/018366 doi: bioRxiv preprint first posted online Apr. 23, 2015; q=4.0x10 -3 ), 'abnormal thermal nociception' (E=2.25, hypergeometric P=5.4x10 -3 , FDR q=0.05), 'abnormal glucose homeostasis' (E=1.46, hypergeometric P=2.6x10 -3 , FDR q=3.2x10 -2 ), and many body mass/weight-related phenotypes (Fig. 2B) . We also inferred the functional significance of fixed, derived loss of function (LOF) substitutions in woolly mammoth genes. We identified a single KEGG term enriched among the genes with LOF substitutions, 'fat digestion and absorption' (E=127.64, hypergeometric P=1.0x10 -4 , FDR q=1.0x10 -4 ), and 48 KO terms enriched among these genes at an FDR≤0.10 ( Fig. 3A) . Enriched KO terms were almost exclusively related to cholesterol, sterol, triglyceride, peer-reviewed)
doi:10.1016/j.celrep.2015.06.027 pmid:26146078 fatcat:f5nefsxf7zcs3hfamquiwee6oy