Biologists have reconstructed the ancient DNA of three mammoths from the Siberian permafrost. The age of two specimens exceeds a million years which makes them the most ancient genetic material ever recovered. The study, which is published in the journal Nature, revealed previously unknown details about the evolution of mammoths.
For example, it turned out that two independent populations of these herbivores lived in the early Pleistocene in the east of Siberia, and the North American mammoths of Columbus are descended from hybrids between these evolutionary lines. In addition, scientists have found that more than a million years ago, the ancestors of woolly mammoths went through several stages of adaptations to life in cold climates.
Thanks to modern technology, specialists have been able to extract and analyze DNA from the remains of long-dead living things from all around the globe. However, existing methods have limitations: it is believed that after 2-2.6 million years, ancient DNA becomes so fragmented that it is no longer possible to restore its integrity. Moreover, the oldest genetic samples available for study are much younger than this theoretical limit. Until now, the ancient record belonged to the DNA of a horse with an age of 780-560 thousand years.
Due to a shortage of DNA samples approaching a million years old, reconstructing the evolutionary history of many species remains problematic. For example, various species of mammoths (Mammuthus primigenius) have inhabited Eurasia and North America since 2.5 million years ago, but the relationship between them is rather poorly understood.
Oldest Mammoth DNA to date
To learn more about the evolution of mammoths, a team led by Tom van der Valk at the Center for Paleogenetics in Stockholm tried to extract DNA from molars of three individuals that lived in the early and middle Pleistocene and were found in permafrost in the northeast of Siberia.
Two specimens, nicknamed 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. 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 was much more damaged than the DNA samples of mammoths from the Late Pleistocene. Nevertheless, using a number of new approaches, the authors were able to restore 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 determine 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.
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 living in later times, the authors came to the conclusion that Adycha and Chukochya belonged to the population that gave rise to all woolly mammoths.
Krestovka, on the other hand, lived even before the separation of the evolutionary lines of woolly mammoths and North American mammoths, that is, before the appearance of mammoths in the New World. Apparently, its branch split from the lines of all other mammoths between 2.66 and 1.78 million years ago.
The results of the analysis indicate that in the early Pleistocene in the east of Siberia at least two isolated populations of mammoths lived (perhaps they were even different species). Krestovka belonged to one of them, and the other, to which Adycha belonged, became the ancestor of woolly mammoths.
How did the North American line of mammoths appear?
Researchers believe that Columbus’s North American mammoths are the result of crossing these two populations. According to their calculations, the contribution of the Krestovka line is 38-43 percent, and the Adycha line – 57-62 percent.
Probably the first mammoths to populate North America about 1.5 million years ago were relatives of Krestovka. Then, about 420 thousand years ago, they were crossed with woolly mammoths, which led to the appearance of Columbus’s mammoths. The initial contribution of both populations to the genome of the hybrid species was approximately equal.
Later, woolly mammoths once again hybridized with the mammoths of Columbus, passing on to the latter additional genetic variants, 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’s mammoths are directly descended from southern mammoths (M. meridionalis).
How did Woolly Mammoths adapt to cold climates?
Additional analysis has revealed more about how woolly mammoths became specialists in surviving cold climates. For this, the authors chose 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 reminiscent of the steppe mammoth) and Chukochya (the early woolly mammoth) already had most of the genetic variants characteristic of the woolly mammoths of the late Pleistocene (their proportion was 85.2 and 88.7 percent, respectively).
Then van der Valk and his co-authors studied 91 genetic variants associated with specific adaptations of woolly mammoths to life in the Arctic. Among them are genes that regulate hair growth, thermoreceptors, white and brown fat accumulation, and circadian rhythms.
It turned out that 87 percent of such genes are present in the Adycha genome, and 89 percent in the Chukochya genome. According to researchers, this means that the steppe mammoths living in Siberia have already acquired long hair and some other physiological adaptations. No traces of rapid selection, which would correspond to the accelerated adaptations to life in the north in the Middle Pleistocene, have been found.
However, 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 the Late Pleistocene woolly mammoths, only two were found in the Chukochya. This indicates that the adaptation to life in the north was a gradual process and continued for hundreds of thousands of years.
When mentioning mammoth DNA, people are primarily interested in the ability to clone these animals. Scientists have been working on this possibility for decades, with the sole purpose of reviving these ancient species.
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