Abstract
Woolly mammoths (Mammuthus primigenius) populated Siberia, Beringia, and North America during the Pleistocene and early Holocene. Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths (Palkopoulou et al. 2015). One mammoth specimen is from a mainland population 45,000 years ago when mammoths were plentiful. The second, a 4300 yr old specimen, is derived from an isolated population on Wrangel island where mammoths subsisted with small effective population size more than 43-fold lower than previous populations. These extreme differences in effective population size offer a rare opportunity to test nearly neutral models of genome architecture evolution within a single species. Using these previously published mammoth sequences, we identify deletions, retrogenes, and non-functionalizing point mutations. In the Wrangel island mammoth, we identify a greater number of deletions, a larger proportion of deletions affecting gene sequences, a greater number of candidate retrogenes, and an increased number of premature stop codons. This accumulation of detrimental mutations is consistent with genomic meltdown in response to low effective population sizes in the dwindling mammoth population on Wrangel island. In addition, we observe high rates of loss of olfactory receptors and urinary proteins, either because these loci are non-essential or because they were favored by divergent selective pressures in island environments. Finally, at the locus of FOXQ1 we observe two independent loss-of-function mutations, which would confer a satin coat phenotype in this island woolly mammoth.
Highlights
Mammoths (Mammuthus primigenius) were among the most populous large herbivores in North America, Siberia, and Beringia during the Pleistocene and early Holocene [1]
We observe an excess of detrimental mutations, consistent with genomic meltdown in woolly mammoths on Wrangel Island just prior to extinction
We observe an excess of deletions, an increase in the proportion of deletions affecting gene sequences, and an excess of premature stop codons in response to evolution under low effective population sizes
Summary
Mammoths (Mammuthus primigenius) were among the most populous large herbivores in North America, Siberia, and Beringia during the Pleistocene and early Holocene [1]. One specimen is derived from the Siberian mainland at Oimyakon, dated to 45,000 years ago [4] This sample comes from a time when mammoth populations were plentiful, with estimated effective population size of Ne = 13,000 individuals [4]. The second specimen is from Wrangel Island off the north Siberian coast [4] This sample from 4,300 years ago represents one of the last known mammoth specimens. This individual comes from a small population estimated to contain roughly 300 individuals [4]. These two specimens offer the rare chance to explore the ways the genome responds to pre-extinction population dynamics
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