A million years before our era

Scientists have reconstructed mammoth DNA older than a million years

Sergey Kolenov, N+1

Biologists have reconstructed the ancient DNA of three mammoths from the Siberian permafrost. The age of two specimens exceeds a million years – and no one has been able to restore such ancient genetic material before. The study, the results of which are published in the journal Nature (van der Valk et al., Million-year-old DNA sheds light on the genomic history of mammoths), allowed us to learn more about the evolution of mammoths. For example, it turned out that in the early Pleistocene, two independent populations of these herbivores lived in eastern Siberia, and the North American mammoths of Columbus descend from hybrids between these evolutionary lines. In addition, scientists have found out that more than a million years ago, the ancestors of woolly mammoths acquired many adaptations to life in a cold climate.

Thanks to modern technologies, specialists have been able to extract and analyze DNA from the remains of long-dead living creatures, from woolly rhinos and Neanderthals to wolves. However, existing methods have limitations: it is believed that in 2-2.6 million years, ancient DNA is so fragmented that it is no longer possible to restore its integrity. At the same time, the oldest genetic samples available for study are much younger than this theoretical limit. Until now, the record of antiquity belonged to the DNA of a horse aged 780-560 thousand years.

Due to the lack of DNA samples whose age would be approaching a million years, the reconstruction of the evolutionary history of many species remains problematic. For example, various mammoth species (Mammuthus) inhabited Eurasia and North America since 2.5 million years ago, but the relationship between them is poorly understood.

To learn more about the evolution of mammoths, a team of specialists led by Tom van der Valk from the Center for Paleogenetics in Stockholm tried to extract DNA from the molars of three individuals who lived in the Early and Middle Pleistocene and found in permafrost in northeastern Siberia. Two specimens, which received the nicknames Krestovka and Adycha (in honor of the rivers near which the finds were made), resemble steppe mammoths (M.trogontherii) in structure, and experts estimate their age at 1.2-1.0 million years.

Reconstruction of the steppe mammoth, the predecessor of the woolly mammoth. However, the third mammoth, Chukochya, is more like a woolly mammoth (M.primigenius).

The age of this specimen is 0.8-0.5 million years.

The genetic material of Krestovka, Adycha and Chukochya turned out to be much more damaged than mammoth DNA samples from the late Pleistocene. Nevertheless, by applying a number of new approaches, the authors were able to reconstruct the complete mitochondrial genomes of all three individuals. In addition, they partially reconstructed the nuclear genomes of mammoths. For Krestovka, scientists have restored 49 million base pairs, for Adycha – 884 million, and for Chukchi – 3.67 billion.

By applying the molecular clock method to the mitochondrial genomes of three mammoths, van der Valk and his colleagues were able to clarify their age. It turned out that all the specimens are older than the initial estimates: Krestovka lived about 1.65 million years ago, Adycha – 1.34 million years ago, and Chukochya – 0.87 million years ago. The analysis based on the nuclear genome, which the authors conducted for Adycha and Chukochya, showed similar results – 1.28 and 0.62 million years, respectively. Thus, the researchers were able to extract DNA from two specimens older than a million years. Previously, this was not possible not only for mammoths, but also for any other fossil animals. 

Thanks to DNA reconstruction, van der Valk's team had the opportunity to learn more about the evolutionary history of the mammoth genus. Comparing the mitochondrial and nuclear DNA of three individuals from the early and Middle Pleistocene with the genetic data of specimens that lived in later times, the authors concluded that Adycha and Chukochya belong to the population that gave rise to all woolly mammoths. But the Krestovka lived even before the separation of the evolutionary lines of woolly mammoths and North American mammoths of Columbus (M.columbi), that is, before the appearance of mammoths in the New World. Apparently, its branch separated from the lines of all other mammoths in the period between 2.66 and 1.78 million years ago.

The results of the analysis indicate that at least two isolated mammoth populations lived in the early Pleistocene in eastern Siberia (perhaps they were even different species). Krestovka belonged to one of them, and the other, to which Adycha belonged, became ancestral to woolly mammoths. Researchers believe that the North American mammoths of Columbus are the result of the crossing of these two populations. According to their calculations, the contribution of the Krestovka line is 38-43 percent, and the Adycha line is 57-62 percent.

Probably, the first mammoths that settled North America about 1.5 million years ago were Krestovka's relatives. Then, about 420 thousand years ago, they crossed with woolly mammoths, which led to the appearance of Columbus mammoths. The initial contribution of both populations to the genome of the hybrid species was approximately equal. Later, woolly mammoths once again hybridized with Columbus mammoths, transferring additional genetic variants to the latter, which made up about twelve percent of the genome. In this case, the gene flow was unidirectional and did not affect woolly mammoths. The results obtained contradict the popular hypothesis that Columbus mammoths are directly descended from southern mammoths (M.meridionalis).

Additional analysis allowed us to learn more about how woolly mammoths became specialists in surviving in cold climates. To do this, the authors selected genetic changes that occurred in Late Pleistocene mammoths compared to Asian and African elephants and affected the production of proteins. It turned out that the Adycha (more like a steppe mammoth) and the Chukchi (early woolly mammoth) already had most of the genetic variants characteristic of woolly mammoths of the late Pleistocene (their share was 85.2 and 88.7 percent, respectively).

Van der Valk and his co-authors then studied 91 genetic variants associated with specific adaptations of woolly mammoths to life in The Arctic. Among them are genes that regulate the growth of wool, the work of thermoreceptors, the accumulation of white and brown fat, as well as circadian rhythms. It turned out that 87 percent of such genes are present in the genome of the Adycha, and 89 percent in the genome of the Chukchi. According to the researchers, this means that steppe mammoths living in Siberia have already acquired long hair and some other physiological adaptations. Traces of rapid selection, which would correspond to accelerated adaptations to life in the north in the Middle Pleistocene, could not be found.

However, the analysis of changes in the well-studied TRPV3 gene, which is responsible for the work of thermoreceptors, paints a more complex picture. Of the four amino acid substitutions characteristic of Late Pleistocene woolly mammoths, only two were found in Chukchi. This indicates that the adaptation of these proboscis to life in the north was a gradual process and lasted for hundreds of thousands of years.

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