Comparative Genomic Study Sheds New Light on Cat Evolution

New research led by Texas A&M University and the University of Missouri scientists explains how cats, including domestic cats, lions, tigers, Geoffroy’s cats and Asian leopard cats, evolved into different species and sheds light on how different genetic changes in cats relate to survival abilities like the ability to smell prey.

“Our goal was to better understand how cats evolved and the genetic basis of the trait differences between cat species,” said Professor Bill Murphy, a researcher at Texas A&M University.

“We wanted to take advantage of some new technologies that allow us to create more complete cat genomic maps.”

Among the things Professor Murphy and colleagues were trying to better understand is why cat chromosomes — cellular structures containing the genetic information for traits like fur color, size, and sensory abilities — are more stable than in other mammal groups.

“We’ve known for a while now that cat chromosomes across species are very similar to each other. For example, the chromosomes of lions and domestic cats hardly differ at all,” Professor Murphy said.

“There appear to be far fewer duplications, rearrangements, and other types of variation than what are commonly found in great apes.”

In the primate order, this kind of genetic variation has led to the evolution of different species — including humans and great apes.

“The great ape genomes tend to break and rearrange, and even human genomes have very unstable regions. These variations may predispose certain individuals to have genetic conditions, like autism and other neurological disorders,” Professor Murphy said.

The key to this variation between cats and apes appears to be the frequency of something called segmental duplications.

“Primate genome researchers have been able to link these segmental duplications to chromosome rearrangements. The more segmental duplications you have in your DNA, the more likely the chromosomes are to rearrange, etc.,” Professor Murphy said.

“What we discovered by comparing a large number of cat species genomes is that cats have just a fraction of the segmental duplications found in other mammal groups — primates actually have seven times more of these duplications than cats. That’s a big difference, and now we believe we understand why cat genomes are more stable.”

While cats may not have as many large genetic rearrangements in their DNA, they still have plenty of differences.

Through their research, the authors now better understand which parts of cat DNA cause those variations, especially the variations that define speciation, or the differences between species.

“It turns out that there’s a large region on the center of the X chromosome where most of the genetic rearrangements are happening,” Professor Murphy said.

“In fact, there’s one specific repetitive element within this region called DXZ4 that evidence tells us is largely responsible for the genetic isolation of at least two cat species, the domestic and jungle cat.”

DXZ4 is a satellite repeat; it’s not a typical gene that codes for a physical trait like fur color, but, rather, it aids in the three-dimensional structure of the X chromosome and likely played an important role in cat speciation.

“We still don’t know the precise mechanism, but by comparing all these cat genomes, we can better measure the rate at which DXZ4 evolved in one species compared to all the others. What we learned is that DXZ4 is one of the most rapidly evolving parts of the cat genome; it’s evolving faster than 99.5% of the rest of the genome,” Professor Murphy said.

“Because of the rate at which it mutates, we were able to demonstrate why DXZ4 is probably linked to speciation.”

Using new, highly detailed genome sequences, Professor Murphy and co-authors also uncovered clearer links between the number of olfactory genes, which govern scent detection in cats and variation in social behavior and how they relate to their surroundings.

“Since cats are predators who rely heavily on smell to detect their prey, their sense of smell is a pretty important part of who they are,” Professor Murphy said.

“Cats are a very diverse family, and we’ve always wanted to understand how genetic variation plays a role in different cat species’ ability to smell in their different environments.”

“Lions and tigers have a pretty big difference between certain odorant genes involved in detecting pheromones, which are chemicals that different animals release into the environment to communicate information about identity, territory, or danger.”

“We think the large difference has to do with lions being very social animals living in family groups and tigers living a solitary lifestyle. Lions may have a reduced reliance on pheromones and other odorants because they’re constantly around other lions, reflected in the fewer genes of this type in their genomes.”

“Tigers, on the other hand, need to be able to smell prey across very large territories as well as find mates.”

“Tigers, in general, have large olfactory and pheromone receptor repertoires. We think this is directly tied to the size of their territories and the variety of environments in which they live.”

“Domestic cats, on the other hand, appear to have lost a wide range of olfactory genes.”

“If they don’t have to travel as far to find what they need because they’re living with people, it makes sense that natural selection wouldn’t preserve those genes.”

One of the most important conclusions from this research is that cat species may be similar in many ways, but their differences matter.

“These differences are showing us how these animals are perfectly suited for their natural environments,” Professor Murphy said.

“They’re not interchangeable, and that’s valuable information for conservationists and others working to preserve or restore species in their natural habitats.”

The findings were published on November 2, 2023 in the journal Nature Genetics.

Citation:

K.R. Bredemeyer et al. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nat Genet, published online November 2, 2023; doi: 10.1038/s41588-023-01548-y

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This article was first published by Sci News on 7 November 2023. Lead Image: The tiger (Panthera tigris). Image credit: Chiem Seherin.