Researchers show that mobile elements frolic in the genome

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OK! The LSU researchers and their international collaborators studied six species of baboons using samples from 19 sites across the African continent. The results reveal a surprising amount of genetic admixture, both ancient and recent, raising the question: What is a species anyway? Photo credit: Science, with drawings of male baboons by Stephen Nash

Baboons (Papio) are found throughout the African continent, from west to east and south. They have canine-like noses, impressive teeth, and a thick coat that varies widely in color between the six species of olive, yellow, chacma, kinda, guinea, and hamadryas. Their habitats range from savannas and scrubland to tropical forests and mountains.

Chacma baboons, the largest weighing up to 100 pounds, are found even in the Kalahari Desert, while the neighboring Kinda baboons, the smallest at around 30 pounds, stay close to water. Most live in large troops of dozens or hundreds of members. While most baboons are polygynandrous, with males and females mating with multiple partners, hamadryas baboons, also known as sacred baboons, live exclusively in single-male, multiple-female units.

In a paper published today in the journal Science titled “Genome-wide Coancestry Reveals Details of Ancient and Recent Male-driven Reticulation in Baboons,” researchers show surprising amounts of genetic mixing between baboon species, something that likely also occurred in early humans. Mark Batzer, Boyd Professor and Dr. Mary Lou Applewhite Distinguished Professor of Biological Sciences at LSU; Jessica Storer, Ph.D., Batzer’s former LSU student and now research associate; and Jerilyn Walker, a research associate at LSU, all contributed to the research. Together, they analyzed the mobile, or “transposable,” genetic elements in samples from 225 baboons from 19 geographic locations.

“Everyone thinks their genome is perfectly stable, and that’s completely wrong,” Batzer said. “Well over half of the genome is inherently fluid, moving within and between individuals, as well as between generations and populations. This mobile part of the genome, or mobilome, provides important clues about how different species are related to each other, how they differ, and if two individuals share a common ancestor.

Whole genome sequencing has revolutionized the amount and detail of genetic diversity that researchers now have to study. While the LSU researchers had previously examined a few hundred mobile elements, or “jumping genes,” mostly of the Alu and L1 types, they were now able to analyze over 200,000 elements computationally, confirming and extending previous studies. The broader research consortium includes more than 30 collaborators around the world and was led by Jeffrey Rogers, Associate Professor of Molecular and Human Genetics at Baylor College of Medicine.

“There are questions that were still science fiction when I started my job and are now quite understandable,” said Batzer. “We also return to this fundamental question: ‘What is a species anyway?’ When I was a young scientist, it meant reproductive isolation; no exchange of genes back and forth, and individuals of different species formed sterile hybrids. Well, this whole concept has evolved, and what we’re seeing now is a free exchange of genes back and forth both anciently and more recently. In other words, there was no linear evolution of genetically isolated species changing over time.”

Mobile, transposable elements cause a subset of all genetic mutations known as structural genetic variants, one of the most important types of mutations in the genome. Therefore, mobile elements account for some, but not all, genetic diversity. Their activity or speed of movement also differs between species, even at different times. For example, while baboons are currently in “fast-forward,” orangutans are almost on a hiatus. Man is somewhere in between.

“You can say that mobile elements like Alu and L1 are involved in a genetic arms race or competition within the genome,” Batzer said. “The mobile elements attempt to multiply while the genome exerts control over this expansion, lest the elements ‘overrun’ the genome and cause so much damage that there is a risk of the host dying. Some mobile elements are distant relatives of viruses, so some of the control systems are the same that control the spread of viruses.”

Apparent similarities, for example between two individuals of the same species, can mask surprising amounts of genetic diversity, since – genetically speaking – a baboon can have almost as much in common with a baboon of a different species. The researchers were also able to show for the first time in non-human primates how the yellow baboons of western Tanzania received genetic input from three different lineages – yellow, olive and kinda.

“This was the first time we’ve seen how three different species contribute to the formation of one, and in detail,” Batzer said. “These high-resolution datasets allow us to draw much more accurate and detailed conclusions from the observations we make.”

Baboons and humans have about 91 percent identical DNA. While differences between humans are relatively small, baboons are more genetically diverse. Larger mobile elements, so-called LINE elements, such as e.g. B. L1, carry around an enzymatic machinery to help them, and the smaller Alu elements mobilize and drive change in mammals (L1) and primates (Alu).

Mobile and transposable elements are inherently diverse and effectively “circle” the genomes of all primates, including humans, as well as other species. The processes by which they affect the genome are called insertional mutagenesis, transduction, and recombination. Tracking the insertions, which is Batzer’s specialty, offers two advantages in establishing common or separate ancestry.

First, the presence of a mobile element at a particular site in the genome constitutes identity by descent; The probability of an exact match without a common ancestry is almost negligible. Second, it is possible to trace insertions back to the point at which they first appeared, thereby ascertaining the ancestral genetic character state and unequivocally anchoring species relationships.

“We now believe that mobile elements are one of the biggest driving forces affecting the genome, not only in primates but also in many mammalian and many non-mammalian systems,” said Batzer.

Next, the LSU research team will study the mobilization and genomic impact of a recently identified transposable element in South American primates.

More information: Erik F. Sørensen et al., Genome-wide coancestry reveals details of ancient and recent male-directed reticulation in baboons, Science (2023). DOI: 10.1126/science.abn8153

Journal Information: Science