Texas A&M researchers use AI to identify genetic ‘time capsule’ that distinguishes species

(Press-News.org) In a groundbreaking study, scientists from the Texas A&M College of Veterinary Medicine and Biomedical Sciences (VMBS) have utilized cutting-edge artificial intelligence methods to identify a region of the X chromosome that has maintained the distinctiveness of mammal species for millions of years.

Their findings shed new light on how species maintain their genetic identity, even when hybridization acts to homogenize their gene pools.

“We know that species like big cats; wolves, dogs and coyotes; and even whales and dolphins have interbred to create hybrid offspring. What has been less clear has been why, despite all this interbreeding, these animals have remained separate species,” said Dr. Nicole Foley, a research assistant professor in the VMBS’ Department of Veterinary Integrative Biosciences and the study’s lead author.  

The mixing of DNA between species is common across the Tree of Life and often helps species survive as they explore new environments and encounter new pathogens or environmental conditions.

A major obstacle has been the lack of detailed genetic recombination maps, which are crucial for understanding how the shuffling of genes during reproduction, together with natural selection, influences the emergence of reproductive barriers in nature. This genetic swapping makes it more challenging for scientists to accurately map out species relationships, which are crucial for understanding the evolutionary history of animals.

Now, using AI-driven genome analysis, researchers can unlock this hidden blueprint of mammalian evolution.

A time capsule in the genome A major discovery from these studies is the identification of a massive region on the X chromosome that is shared across most mammalian species for more than 100 million years.

Dubbed the X-linked recombination desert (XLRD), this region spans nearly 30% of the X chromosome. It serves as a powerful reproductive barrier and plays a crucial role in preserving the true evolutionary relationships among species, even when widespread genetic exchange clouds the rest of the genome.

“Remarkably, the XLRD appears to be a recurrent and ancient feature in mammals, functioning almost like a genomic ‘time capsule’ that records deep evolutionary history,” Foley said.

“We were unable to see this before because we never had this diversity of recombination maps,” she said. “When we lined up all of the X chromosomes for those 22 species and we looked at the recombination map, it was pretty much the same map — it dipped in the exact same place, so we knew there was something functionally important going on in this part of the chromosome.”

“We had some evidence from previous studies based on a small handful of species that the XLRD exists, but we were very surprised to discover that this region was so conserved and so ancient,” said Dr. Bill Murphy, a distinguished professor in the VMBS and director of the Texas A&M Center for Comparative Genomics.

This discovery was especially exciting because the XLRD appears to play a key role in speciation — the process by which one species evolves into distinct new species through the development of reproductive barriers.

The XLRD’s reproductive role The researchers also discovered that the XLRD region is notably enriched with genes related to male and female reproduction and sex chromosome silencing; this suggest that genetic switches relevant to X chromosome regulation in both sexes, which are embedded within and around the XLRD, may play a larger role in infertility as well as in human conditions like polycystic ovarian syndrome, an endocrine disorder that has been linked to reproductive and metabolic issues.

“This is one of the more novel findings because it has been thought that reproductive barriers arise rapidly and from unique genetic sources across different groups of species. Our results suggest this is not the case,” Murphy said. “For all the reasons, it looks like the XLRD is a key region associated with reproductive dysfunction in hybrids and reproductive isolation in nature.”

These discoveries open new avenues for understanding problems — and finding solutions — related to human reproduction and fertility.

By Texas A&M University College of Veterinary Medicine and Biomedical Sciences

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