NEW YORK – Using ancient genome sequences for nearly two-dozen woolly mammoths (Mammuthus primigenius) going back 700,000 years, an international team led by investigators in Sweden has tallied the genetic changes that appear to have helped the woolly mammoth adapt to its frigid environment, including features that continued to evolve in the animal over time.
"We found some highly evolved genes related to fat metabolism and storage that are also found in other Arctic species like reindeer and polar bears, which means there's probably convergent evolution for these genes in cold-adapted mammals," first- and co-corresponding author David Díez-del-Molino, a researcher affiliated with Stockholm's Center for Paleogenetics, Stockholm University, and the Swedish Museum of Natural History, said in a statement.
As they reported in Current Biology on Friday, the researchers sequenced the whole genomes of 16 Siberian woolly mammoths, while generating new sequence data for a 700,000-year-old woolly mammoth known as the Chukochya woolly mammoth that was analyzed in the past. Those genomes were analyzed alongside half a dozen previously sequenced woolly mammoth representatives dated to the last 100,000 years.
"Having the Chukochya genome allowed us to identify a number of genes that evolved during the lifespan of the woolly mammoth as a species," co-senior and co-corresponding author Love Dalén, an evolutionary genomics researcher at the Center for Paleogenetics, said in a statement. "This allows us to study evolution in real time, and we can say these specific mutations are unique to woolly mammoths, and they didn't exist in its ancestors."
Along with analyses focused on finding genetic changes in the woolly mammoth over time, the team compared the mammoth genomes to sequences for 21 African elephants and seven Asian elephants and performed phylogenetic analyses that also included data on the American mastodon.
Starting with ancestral alleles that are shared in the African and Asian elephants, the investigators highlighted nearly 1.2 million derived variants in the woolly mammoth genome, focusing in on mammoth genes affected by non-synonymous, derived variants that appeared to alter protein function and contribute to woolly mammoth evolution.
In the process, the researchers flagged genes with ties to noted mammoth features, such as their long fur and extensive fat reserves, together with more subtle cold adaptations involving genes contributing to lipid metabolism, thermal sensation, and other sensory processes — adaptations that started more than 700,000 years ago and were present in the oldest mammoth analyzed.
The team tracked down fixed-derived, non-synonymous variants in skin and hair development genes, for example, including genes linked to "uncombable hair syndrome" and other hair-related conditions in humans. It also unearthed signs of positive selection falling in or around genes associated with the fat metabolism in polar bears and reindeer, pointing to potential convergence across different cold-adapted animals.
The Chukochya individual carried almost 92 percent of the protein-coding mutations found in more recent mammoth representatives, though evolution continued over time and was reflected in genetic differences between the 700,000-year-old mammoth and woolly mammoths from the last 100,000 years.
In particular, the researchers saw more recent selection on body size, skeletal features, ear size, and immune-related genes, as well as continued adaptation of earlier woolly mammoth features via selection on distinct genes. They further dug into variation between animals to rule out processes that did not seem to have pronounced evolutionary effects, despite differing from elephant sequences.
"We found that some of the genes that were previously thought to be special for woolly mammoths are actually variable between mammoths, which means they probably weren't as important," Díez-del-Molino said.