Mobile elements, also known as transposable elements or jumping genes, are DNA segments that can move within a genome. They’ve been discovered in a variety of organisms, including humans, and are thought to be important drivers of genetic diversity and evolution.
Whole-genomic sequencing has transformed the amount and detail of genetic diversity that researchers can now study. While the researchers had previously examined a few hundred mobile elements or ‘jumping genes,’ primarily of the Alu and L1 types, they were now able to computationally analyze over 200,000 elements, confirming and expanding on previous research. Their findings add to the evidence of species fluidity and the continuous spread of mobile and transposable genetic elements.
Baboons (Papio) can be found throughout Africa, from west to east and south to north. They have dog-like noses, impressive teeth, and thick fur that varies in color between the six species: olive, yellow, chacma, Kinda, Guinea, and hamadryas. Their natural environments range from savannas and bushlands to tropical forests and mountains.
Chacma baboons, the largest at up to 100 pounds, can even be found in the Kalahari Desert, whereas Kinda baboons, the smallest at around 30 pounds, prefer to live near water. The majority live in large troops of dozens or hundreds of people. While most baboons are polygynandrous, with males and females mating with multiple partners, hamadryas baboons, also known as sacred baboons, only live in groups of one male and multiple females.
Everybody believes their genome is perfectly stable, and that’s exactly wrong. Well over half of the genome is fluid in nature and moves around in and between individuals, and between generations and populations.
Chacma baboons
Researchers show surprising amounts of genetic admixture between baboon species in their paper “Genome-wide Coancestry Reveals Details of Ancient and Recent Male-driven Reticulation in Baboons,” which was published in the journal Science. Mark Batzer, Boyd Professor and Dr. Mary Lou Applewhite Distinguished Professor of Biological Sciences at LSU, Jessica Storer, PhD, a former student of Batzer’s at LSU and now research scientist, and LSU research associate Jerilyn Walker all contributed to the study. They examined the mobile or “transposable” genetic elements in 225 baboon individuals from 19 different geographic locations.
“Everybody believes their genome is perfectly stable, and that’s exactly wrong,” Batzer said. “Well over half of the genome is fluid in nature and moves around in and between individuals, and between generations and populations. This mobile part of the genome, or mobilome, provides important clues as to how different species are related to one another, how they differ and when two individuals share a common ancestor.”
Whole-genomic sequencing has transformed the amount and detail of genetic diversity that researchers can now study. While the LSU researchers had previously examined a few hundred mobile elements or “jumping genes,” primarily of the Alu and L1 types, they were now able to computationally analyze over 200,000 elements, confirming and expanding on previous research. The larger research consortium, led by Jeffrey Rogers, associate professor of molecular and human genetics at Baylor College of Medicine, includes more than 30 collaborators from around the world.
“There are questions that were science fiction when I first started in the field that are now perfectly approachable,” said Batzer. “We’re also reminded of the fundamental question, ‘What even is a species?'” It meant reproductive isolation when I was a young scientist; no gene exchange, and individuals from different species would form infertile hybrids. That concept has evolved, and we now see free exchanges of genes back and forth, both in ancient and modern times. In other words, there hasn’t been a straight line of genetically isolated species changing over time.”
One of the most important types of mutation in the genome is caused by mobile, transposable elements, which cause a subset of all genetic mutations known as structural genetic variants. As a result, mobile elements account for some genetic diversity but not all differences. Their activity, or rate of movement, varies between species, as well as at different times. While baboons are currently on “fast forward,” orangutans, on the other hand, are almost on pause. Humans fall somewhere in the middle.
“You can say 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 expand in number, while the genome exerts control over that expansion, so the elements don’t ‘overrun’ the genome and cause so much havoc it risks killing the host. Some mobile elements are distant relatives of viruses, so some of the control systems are the same ones that control the spread of viruses.”
Apparent similarities, such as those between two individuals of the same species, can conceal surprising amounts of genetic diversity, as one baboon can share nearly as much genetically with a baboon of a different species. For the first time in non-human primates, the researchers were able to demonstrate how yellow baboons in western Tanzania received genetic input from three distinct lineages: yellow, olive, and Kinda.
“This was the first time we’d seen three different species contribute to the genesis of one, and we’ve done it in detail,” Batzer said. “These high-resolution data sets allow us to draw much more accurate and detailed conclusions from the observations we make.”
Baboons and humans share approximately 91 percent of their DNA. Baboons are genetically more diverse than humans, which have relatively little variation. Larger mobile elements known as LINE elements, such as L1, carry enzymatic machinery that aids them in mobilizing and driving change in mammals (L1) and primates (Alu).
Mobile and transposable elements are diverse in and of themselves, effectively “monkeying around” the genomes of all primates, including humans, and other species. Insertional mutagenesis, transduction, and recombination are the processes by which they affect the genome. Batzer’s specialty, tracking insertions, provides two advantages in determining shared or separate ancestry. First, the presence of a mobile element at a specific location in the genome represents identity by descent; the likelihood of an exact match in the absence of shared ancestry is near zero. Second, insertions can be traced back to their origin, establishing the ancestral genetic character state and unambiguously rooting species relationships.
“We now believe mobile elements are one of the single biggest driving forces impacting genomes, and not just among primates, but across many mammals and many non-mammalian systems as well,” Batzer said.
