DNA analysis of museum specimens reveals evolutionary story

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Museum specimens held in natural history collections around the world represent a wealth of genetic information that is underutilized due to the poor state of DNA preservation, which often makes sequencing difficult. An international team, led by researchers from the University of Geneva (UNIGE) and the Natural History Museum of the City of Geneva (MHN), optimized a method developed to analyze ancient DNA in order to identify relationships between species on a deep evolutionary scale. This work is published in the journal Biology and evolution of the genome.

By combining and comparing the sequences of a large number of genes or complete genomes, it is possible to establish links between related species and to trace the main stages in the evolution of organisms from a common ancestor. These phylogenomic studies are based on the amplification and sequencing of DNA fragments, followed by bioinformatic analyzes to compare the sequences. They therefore generally require carefully sampled DNA in a good state of preservation.

Decipher degraded DNA

For this reason, most of the specimens kept in natural history museums have not yet revealed all their secrets, because in most cases DNA is often very degraded and difficult to sequence. An international team led by Emmanuel Toussaint, researcher at MHN, and Nadir Alvarez, researcher at the Department of Genetics and Evolution of the Faculty of Sciences of UNIGE and chief curator at MHN, has developed a method already used for samples. in order to apply it to very fragmented DNA due to partial degradation. The HyRAD-X technique involves harvesting pieces of the genome to be analyzed with DNA probes from closely related species, then sequencing them to detect the differences between the genomes. However, these DNA probes are only effective hooks for closely related genomes and this technique has so far not been able to follow the evolution of a single species over time.

In this work, the scientists used HyRAD-X RNA probes instead of DNA probes to find fragments of interest in the genome. RNAs, copies of DNA molecules responsible for transferring information encoded by the genome, have a very strong affinity for DNA, and RNA-DNA pairings occur more easily than DNA-DNA pairings. RNA probes are therefore more efficient hooks, especially when the genomes to be analyzed exhibit significant levels of divergence. “Thanks to this new method, we were able to trace the history of evolution, not within a single species over a million years, but within several species and over tens of millions of years. ! explains Emmanuel Toussaint, first author of the study.

The better known genealogy of the ground beetle

The researchers were particularly interested in specimens of a beetle emblematic of the island of Saint Helena in the middle of the Atlantic Ocean, collected in the 1960s and kept at the MHN in Geneva. Analysis of the DNA of these beetles revealed that this species, now extinct and so far classified in the genus Aplothorax, actually belongs to the genus Calosoma. It also made it possible to locate its biogeographical origin, probably in Africa, and to generate the chronology of the evolution of the Carabinae subfamily, the origin of which dates back to the Lower Cretaceous. “Our study opens up many perspectives for establishing the evolutionary history of millions of specimens in museum collections around the world,” concludes Nadir Alvarez.

Reference: Toussaint EFA, Gauthier J, Bilat J, et al. HyRAD-X exome capture museomics unveils the evolution of giant beetles. Genome Biol. Evol. 2021; (evab112). doi: 10.1093 / gbe / evab112

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