The woolly mammoth (Mammuthus primigenius) is ideal for making direct observations of the evolution of a mammalian genome and its genes as a species struggles to adapt to environmental changes, ending with extinction of the lineage. Because of the many well preserved specimens, their wide distribution in time and space, and the extensive literature on the species and its habitat, mammoths are the best model system for studying DNA from extinct species. Over the last four years, the field of ancient DNA has been revolutionized by novel sample-preparation methods and next-generation DNA sequencing, resulting in genome-scale projects, as well as population genetic studies based on complete mitochondrial sequences for the woolly mammoth. A recent analysis of these mitochondrial DNA sequences detected a deep split in the woolly mammoth population that has not been observed in the fossil record. Still more recently, a preliminary survey of the mammoths full DNA complement suggested that the split can be observed in two particular specimens, called M4 and M25 for historical reasons. These observations, though quite limited and preliminary, lead to the hypotheses that the woolly mammoth clades exemplified by M4 and M25 were genetically quite distinct, separating over a million years ago, and that M25s clade became extinct well before coming into contact with humans. The methods employed in this project will refine genomic sequencing and ultimately lead to a greater understanding of wooly mammoth genomic evolution over the last 100,000 years. The PIs have published initial results in the November, 2008 issue of Nature. The publication brought broad press coverage and has since been incorporated into secondary school teaching. This research has proven to be transformative not only in its scientific results but its stimulation of the scientific and lay public communities.
Asian elephants and woolly mammoths are characterized by major differences in their appearance. They also inhabited different climatic zones and therefore had to adapt in order to flourish in very different environments. We determined the nuclear genome sequences of multiple individuals from each of the two species. For this undertaking DNA was isolated from blood in case of the Indian elephant and from preserved hair for the woolly mammoth. We then searched for the molecular mechanisms that potentially underpin the adaptation of woolly mammoths to frigid environments in contrast to African and Asian elephants. Our computational analysis of the three elephant genomes shows genomic differences unique to the mammoth lineage and highlights proteins that modulate physiological and behavioral responses to external temperature. To test our computational predictions, we experimentally validated an amino-acid substitution in an otherwise highly conserved region of the mammoth ion-channel protein TRPV3. To experimentally test the function of the newly generated protein, a version of the TRPV3 gene carrying the mammoth genotype had to be genetically engineered in a mouse model. It could be shown that the new genotype had a strong effect on the temperature sensitivity of the mouse. This study therefore shows that sequencing whole genomes allows in an unbiased fashion one can unravel genotype-phenotype relationships, even with an extinct species.
