Oldest DNA sequences reveal how mammoths evolved

This illustration represents a reconstruction of the steppe mammoths that preceded the woolly mammoth, based on genetic analysis of ancient mammoth DNA. (Illustration by Beth Zaiken/Centre for Palaeogenetics) 

An international team of scientists has sequenced DNA recovered from mammoth remains as old as 1.2 million years. The analyses show that the Columbian mammoth that inhabited North America during the last ice age was a hybrid between the woolly mammoth and a previously unknown genetic lineage of mammoth.

Researchers were able to analyze the genomes from three ancient mammoths using DNA recovered from mammoth teeth that had been buried in the Siberian permafrost for 0.7 to 1.2 million years. 

The study, led by researchers at the Centre for Palaeogenetics in Stockholm and published February 17 in Nature, also provides new insights into when and how fast mammoths became adapted to cold climate.

Coauthor Beth Shapiro, professor of ecology and evolutionary biology at UC Santa Cruz, said the results “push back pretty substantially what we’d come to think of as the oldest possible ancient DNA.” The previous record was DNA from a 750,000-year-old horse, which Shapiro’s team analyzed in 2013.

In the new study, researchers were able to analyze the genomes from three ancient mammoths, using DNA recovered from mammoth teeth that had been buried in the Siberian permafrost for 0.7 to 1.2 million years. Around one million years ago there were no woolly or Columbian mammoths, as they had not yet evolved. This was the time of their predecessor, the ancient steppe mammoth.

This is the first time that DNA has been sequenced and authenticated from million-year-old specimens, and extracting the DNA from the samples was challenging. The scientists found that only minute amounts of DNA remained in the samples and that the DNA was degraded into very small fragments.

“This DNA is incredibly old. The samples are a thousand times older than Viking remains, and even pre-date the existence of humans and Neanderthals”, said senior author Love Dalén, professor of evolutionary genetics at the Centre for Palaeogenetics in Stockholm.

The age of the specimens was determined using both geological data and the molecular clock. The analyses showed that two of the specimens are more than one million years old, whereas the third is roughly 700 thousand years old and represents one of the earliest known woolly mammoths.

“We could tell from the geological and paleontological context that they were old, but we couldn't say with certainty how old,” Shapiro said. “Fortunately, the DNA itself provides some clues. Because changes to the genome accumulate in a clock-like way, we could count the differences between these old mammoth genomes and other mammoth genomes (from mammoths that lived sufficiently recently that we can date their bones), and use this to approximate how long ago these old mammoths lived.”

Unexpected origin

Analyses of the genomes showed that the oldest specimen, which was approximately 1.2 million years old, belonged to a previously unknown genetic lineage of mammoth. The researchers refer to this as the Krestovka mammoth, based on the locality where it was found. The results show that the Krestovka mammoth diverged from other Siberian mammoths more than two million years ago.

“This came as a complete surprise to us,” said lead author Tom van der Valk. “All previous studies have indicated that there was only one species of mammoth in Siberia at that point in time, called the steppe mammoth. But our DNA analyses now show that there were two different genetic lineages, which we here refer to as the Adycha mammoth and the Krestovka mammoth. We can’t say for sure yet, but we think these may represent two different species.”

The researchers also suggest that it was mammoths that belonged to the Krestovka lineage that colonized North America some 1.5 million years ago. In addition, the analyses show that the Columbian mammoth that inhabited North America during the last ice age was a hybrid. Roughly half of its genome came from the Krestovka lineage and the other half from the woolly mammoth.

“This is an important discovery. It appears that the Columbian mammoth, one of the most iconic Ice Age species of North America, evolved through a hybridization that took place approximately 420,000 years ago”, said co-lead author Patrícia Pečnerová.

Evolution and adaptation

The second million-year-old genome, from the Adycha mammoth, appears to have been ancestral to the woolly mammoth. The researchers could therefore compare its genome with the genome from one of the earliest known woolly mammoths that lived 0.7 million years ago, as well as with mammoth genomes that are only a few thousand years old. This made it possible to investigate how mammoths became adapted to a life in cold environments and to what extent these adaptations evolved during the speciation process.

The analyses showed that gene variants associated with life in the Arctic, such as hair growth, thermoregulation, fat deposits, cold tolerance, and circadian rhythms, were already present in the million-year-old mammoth, long before the origin of the woolly mammoth. These results indicate that most adaptations in the mammoth lineage happened slowly and gradually over time.

“Access to such ancient evolutionary history allows us to discover even more about how evolution works,” Shapiro said. “There were at least two lineages of mammoths that lived in Siberia during the Middle Pleistocene, and both of these lineages contributed ancestry to mammoths that lived in North America.”

Future research

The new results open the door for a broad array of future studies on other species. About one million years ago was a period when many species expanded across the globe. This was also a time period of major changes in climate and sea levels, as well as the last time that Earth’s magnetic poles changed places. Because of this, the researchers think that genetic analyses on this time scale have great potential to explore a wide range of scientific questions.

“One of the big questions now is how far back in time we can go. We haven’t reached the limit yet. An educated guess would be that we could recover DNA that is two million years old, and possibly go even as far back as 2.6 million. Before that, there was no permafrost where ancient DNA could have been preserved,” said Anders Götherström, a professor in molecular archaeology and joint research leader at the Centre for Palaeogenetics.

The study is the result of an international collaboration involving 22 scientists from nine countries. In addition to researchers from UC Santa Cruz and the Centre for Palaeogenetics, a joint research centre funded by Stockholm University and the Swedish Museum of Natural History, the study also includes researchers from the Russian Academy of Sciences, the Natural History Museum and The Crick Institute in the United Kingdom, Potsdam University in Germany, China Agricultural University, the Middle East Technical University in Turkey, the Arctic University of Norway, and the University of Copenhagen in Denmark.

Publication: Beth Shapiro, et al., Million-year-old DNA sheds light on the genomic history of mammoths, nature (2023). DOI: 10.1038/s41586-021-03224-9

Original Story Source: UC SANTA CRUZ