RNA for the first time recovered from an extinct species

A new study shows the isolation and sequencing of more than a century-old RNA molecules from a Tasmanian tiger specimen preserved at room temperature in a museum collection. This resulted in the reconstruction of skin and skeletal muscle transcriptomes from an extinct species for the first time. The researchers note that their findings have relevant implications for international efforts to resurrect extinct species, including both the Tasmanian tiger and the woolly mammoth, as well as for studying pandemic RNA viruses.

The Tasmanian tiger, also known as the thylacine, was a remarkable apex carnivorous marsupial that was once distributed all across the Australian continent and the island of Tasmania. This extraordinary species found its final demise after European colonization, when it was declared as an agricultural pest and a bounty of £1 per each full-grown animal killed was set by 1888. The last known living Tasmanian tiger died in captivity in 1936 at the Beaumaris Zoo in Hobart, Tasmania.

Recent efforts in de-extinction have focused on the Tasmanian tiger, as its natural habitat in Tasmania is still mostly preserved, and its reintroduction could help recovering past ecosystem equilibriums lost after its final disappearance. However, reconstructing a functional living Tasmanian tiger not only requires a comprehensive knowledge of its genome (DNA) but also of tissue-specific gene expression dynamics and how gene regulation worked, which are only attainable by studying its transcriptome (RNA).

"Resurrecting the Tasmanian tiger or the woolly mammoth is not a trivial task, and will require a deep knowledge of both the genome and transcriptome regulation of such renowned species, something that only now is starting to be revealed," says Emilio Mármol, the lead author of a study recently published in the Genome Research journal by researchers at SciLifeLab in collaboration with the Centre for Palaeogenetics, a joint venture between the Swedish Museum of Natural History and Stockholm University.

RNA molecules recovered from the Tasmanian tiger

The researchers behind this study have sequenced, for the first time, the transcriptome of the skin and skeletal muscle tissues from a 130-year-old desiccated Tasmanian tiger specimen preserved at room temperature in the Swedish Museum of Natural History in Stockholm. This led to the identification of tissue-specific gene expression signatures that resemble those from living extant marsupial and placental mammals.

The recovered transcriptomes were of such good quality that it was possible to identify muscle- and skin-specific protein coding RNAs, and led to the annotation of missing ribosomal RNA and microRNA genes, the later following MirGeneDB recommendations.

"This is the first time that we have had a glimpse into the existence of thylacine-specific regulatory genes, such as microRNAs, that got extinct more than one century ago," says Marc R. Friedländer, Associate Professor at the Department of Molecular Biosciences, The Wenner-Gren Institute at Stockholm University and SciLifeLab.

This pioneering study opens up new exciting opportunities and implications for exploring the vast collections of specimens and tissues stored at museums across the globe, where RNA molecules might await to be uncovered and sequenced.

"In the future, we may be able to recover RNA not only from extinct animals, but also RNA virus genomes such as SARS-CoV2 and their evolutionary precursors from the skins of bats and other host organisms held in museum collections," says Love Dalén, Professor of evolutionary genomics at Stockholm University and the Centre for Palaeogenetics.

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Bronze Age family systems deciphered: Mainz palaeogeneticists analyse a 3,800-year-old extended family

The diversity of family systems in prehistoric societies has always fascinated scientists. A groundbreaking study by Mainz anthropologists and an international team of archaeologists now provides new insights into the origins and genetic structure of prehistoric family communities.

Researchers Jens Blöcher and Joachim Burger from Johannes Gutenberg University Mainz (JGU) have analysed the genomes of skeletons from an extended family from a Bronze Age necropolis in the Russian steppe. The 3,800-year-old "Nepluyevsky" burial mound was excavated several years ago and is located on the geographical border between Europe and Asia. Using statistical genomics, the family and marriage relationships of this society have now been deciphered. The study was carried out in cooperation with archaeologists from Ekaterinburg and Frankfurt a. M. and was partly financially supported by the German Research Foundation (DFG) and the Russian Science Foundation (RSCF).

The kurgan (burial mound) investigated was the grave of six brothers, their wives, children and grandchildren. The presumably oldest brother had eight children with two wives, one of whom came from the Asian steppe regions in the east. The other brothers showed no signs of polygamy and probably lived monogamously with far fewer children.

Fascinating snapshot of a prehistoric family

"The burial site provides a fascinating snapshot of a prehistoric family," explains Jens Blöcher, lead author of the study. "It is remarkable that the first-born brother apparently had a higher status and thus greater chances of reproduction. The right of the male firstborn seems familiar to us, it is known from the Old Testament, for example, but also from the aristocracy in historical Europe."

The genomic data reveal even more. Most women buried in the kurgan were immigrants. The sisters of the buried brothers, in turn, found new homes elsewhere. Joachim Burger, senior author of the study, explains: "Female marriage mobility is a common pattern that makes sense from an economic and evolutionary perspective. While one sex stays local and ensures the continuity of the family line and property, the other marries in from the outside to prevent inbreeding."

The genomic diversity of the prehistoric women was higher than that of the men

Accordingly, the Mainz population geneticists found that the genomic diversity of the prehistoric women was higher than that of the men. The women who married into the family thus came from a larger area and were not related to each other. In their new homeland, they followed their husbands into the grave. From this the authors conclude that in Nepluyevsky there was both "patrilineality", i.e. the transmission of local traditions through the male line, and "patrilocality", i.e. the place of residence of a family is the place of residence of the men.

"Archaeology shows that 3,800 years ago, the population in the southern Trans-Ural knew cattle breeding and metalworking and subsisted mainly on dairy and meat products," comments Svetlana Sharapova, archaeologist from Ekaterinburg and head of the excavation, adding, "the state of health of the family buried here must have been very poor. The average life expectancy of the women was 28 years, that of the men 36 years."

In the last generation, the use of the kurgan suddenly stopped and almost only infants and small children were found. Sharapova adds, "it is possible that the inhabitants were decimated by disease or that the remaining population went elsewhere in search of a better life."

Multiple partners and many children for the putative firstborn son

"There is a global connection between different family systems and certain forms of life-style and economy," says Blöcher. "Nevertheless, human societies are characterised by a high degree of flexibility." He adds, "in Nepluyevsky, we find evidence of a pattern of inequality typical of pastoralists: multiple partners and many children for the putative firstborn son and no or monogamous relationships for most others."

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