The record for sequencing the oldest DNA is now held by ancient mammoth DNA over one million years old, breaking the previous record from a horse leg bone estimated at 560,000 – 780,000 years old. The problem with sequencing ancient DNA is that it degrades over time, leaving shorter and shorter fragments that are harder to piece together. Many samples taken from permafrost have previously been found to have too little DNA for sequencing, and it has to have been permanently frozen to stand a chance. Because of the need for consistent permafrost, the theoretical limit for DNA sequencing is estimated at 2.6 million years old due to the geological conditions.
Mammoths first arose around five million years ago in Africa and colonised most of the Northern Hemisphere. Three mammoth teeth were analysed that were excavated from north-eastern Siberia in the 1970s. Once extracted and sequenced, the mammoth DNA was aligned to a modern-day elephant genome, which is similar enough to help reconstruct the order of the sequence. The researchers were able to construct complete mitochondrial genomes for all three of the samples. However, from the main genome, they were only able to recover 49 million base pairs from the oldest sample, compared to 3,671 million base pairs from the youngest.
The samples have been named after the places where they were excavated. The youngest sample, the Chukochya specimen, is 500,000 – 600,000 years old. The shape of the teeth predicted that it was from an early form of the woolly mammoth, and the DNA sequencing supported this. The next sample, the Adycha specimen, also matched the prediction from its shape. It comes from a steppe mammoth, a European species ancestral to the woolly mammoth, 1 – 1.3 million years old. The upper age of these estimations come from genetic dating. The age of the DNA is estimated by looking at the variants in the mammoth DNA compared to a modern-day elephant, and assuming that there has been a constant mutation rate over the last million years. The lower age of the estimations comes from the sediments where the samples were found.
However, the third and oldest specimen from Krestovka is more exciting. It is estimated to be between 1.1 and 1.65 million years old and when the DNA was examined it turned out to be from a previously unknown lineage. It was thought that the Columbian mammoth evolved from steppe mammoths when they colonised North America, with a separate line establishing woolly mammoths. This new DNA has shown that Columbian mammoths actually arose from a mixture of lineages around 420,000 years ago, much more recently than previously estimated. This is the first evidence of hybrid speciation from ancient DNA, showing that Columbian mammoths came from a mixture of woolly mammoths and the newly discovered Krestovka lineage. The analysis also shows another later mixture with woolly mammoths.
Another benefit of the study is it has given more information about how mammoths adapted. This ancient DNA has shown that the early mammoths in Siberia had already evolved many of the traits needed for cold adaptation, such as the woolly fur, which had been thought to come much later. The study is an exciting new development in studying mammoth evolution. But more than that, it proves that sequencing ancient DNA is possible, and there may be many more discoveries waiting in the genomes of other ancient species.
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