Together with an interdisciplinary team of collaborators, researchers at
the Texas A&M School of Veterinary Medicine & Biomedical Sciences
(VMBS) have unearthed new information about the history of cat evolution.
This information explains how cats, including well-known species like
tigers, lions, and domestic cats, evolved into different species and sheds
light on the relationship between various genetic changes in cats and
survival skills like the ability to smell prey.
The effort, which was published today in
Nature Genetics, compared the genomes of numerous cat species to help researchers
understand why, compared to other animal groups like primates, cat genomes
often feature less complicated genetic changes (such rearrangements of DNA
segments). It also provided fresh information on the regions of the cat's
DNA that are most prone to evolve quickly and their function in species
differentiation.
Specializing in cat evolution, Dr. Bill Murphy is a professor of veterinary
integrative biosciences at VMBS. "Our goal was to better understand how cats
evolved and the genetic basis of the trait differences between cat species,"
Murphy stated. "In order to produce more comprehensive cat genomic maps, we
sought to make use of certain novel technologies.
"Our findings will open doors for people studying feline diseases,
behavior, and conservation," he stated. "They'll be working with a more
complete understanding of the genetic differences that make each type of cat
unique."
Different takes on a topic
The reason why feline chromosomes—cellular structures that carry the
genetic information for characteristics like fur color, size, and sensory
abilities—are more stable than those of other animal groups is one of the
many mysteries the scientists were attempting to solve.
"We've known for a while now that cat chromosomes across species are very
similar to each other," Murphy stated. For instance, there is very little
genetic difference between domestic cats and lions. Compared to what is
often observed in big apes, there seem to be considerably fewer
duplications, rearrangements, and other forms of variation."
This type of genetic variety in the primate order has facilitated the
evolution of several species, including great apes and humans.
"The great ape genomes tend to break and rearrange, and even human genomes
have very unstable regions," Murphy stated. "These variations may predispose
certain individuals to have genetic conditions, like autism and other
neurological disorders."
Murphy discovered that the frequency of something called segmental
duplications—DNA segments that are extremely close copies of other DNA
segments found elsewhere in the genome—seems to be the key to this variance
between cats and apes.
"Primate genome researchers have been able to link these segmental
duplications to chromosome rearrangements," he stated. The likelihood of
chromosomal rearrangements increases with the number of segmental
duplications present in an individual's DNA, and so forth.
By analyzing the genomes of many different cat species, we found that
whereas primates have seven times more segmental duplications than cats,
cats only have a small percentage of these duplications compared to other
animal groups. We think we now understand why cat genomes are more
stable—that's a significant distinction," the speaker stated.
A needle with two helixes
Even while there aren't as many significant genetic rearrangements in the
DNA of cats, there are still a lot of distinctions. Murphy and his
associates now have a clearer understanding of which regions of the cat's
DNA are responsible for these alterations, particularly those that
characterize speciation, or the distinctions between species, thanks to
their study.
"It turns out that there's a large region on the center of the X chromosome
where most of the genetic rearrangements are happening," Murphy stated. "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."
Murphy refers to DXZ4 as a satellite repeat; rather than being a normal
gene that codes for a physical characteristic such as fur color, it helps
with the three-dimensional structure of the X chromosome and most likely
contributed significantly to the speciation of cats.
"The exact process is still unknown, but by comparing the genomes of all
these cats, we can estimate more accurately how quickly DXZ4 developed in
one species relative to all the others. We have discovered that DXZ4 is one
of the cat genome's fastest-evolving regions; it is changing at a rate that
surpasses that of 99.5% of the entire genome," the scientist stated.
"Because of the rate at which it mutates, we were able to demonstrate why
DXZ4 is probably linked to speciation," Murphy stated.
Identifying hidden genes
The scientists also discovered stronger connections between the quantity of
olfactory genes, which control smell perception in cats, and variations in
social behavior and how they interact with their environment by using new,
extremely precise genome sequences.
"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," Murphy
stated. "We've long wanted to know how genetic diversity affects the ability
of different cat species to smell in their various habitats since cats are a
highly varied family.
"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," he said.
"We believe that the main distinction between the two species is that
tigers lead solitary lives whereas lions are very gregarious animals that
live in family groupings. Because they are in close proximity to other
lions, lions may be less dependent on pheromones and other odorants, as seen
by the lower number of these genes in their genomes, the expert
speculated.
In contrast, tigers must be able to locate potential mates and detect prey
across vast distances.
"Tigers, in general, have large olfactory and pheromone receptor
repertoires," Murphy said. "We think this is directly tied to the size of
their territories and the variety of environments in which they live."
In contrast, a large variety of olfactory genes seem to have disappeared
from domestic cats.
"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," he stated.
Murphy said that the odorant receptors from the fishing cat, a kind of wild
cat native to Southeast Asia that has evolved to life in the water, are his
favorite example from the study.
"We were able to show that fishing cats have retained many genes for
detecting waterborne odorants, which is a pretty rare trait in terrestrial
vertebrates," he stated. "All of the other cat species have lost these
specific genes over time, but fishing cats still have them."
This new understanding of the cat olfactory genes was made possible by trio
binning, a novel method of genome sequencing that enables researchers to
read the most challenging parts of a genome.
Also, the new technique greatly simplifies the process of distinguishing
paternal and maternal DNA.
"With trio binning, you can now take DNA from an F1 hybrid—an animal whose
DNA is split 50-50 between parents of different species—and cleanly separate
the maternal and paternal DNA, giving you two complete sets of DNA, one for
each parent species," Murphy stated. "The process is much simpler, and the
results are more complete."
Completing the gaps
The project's most significant finding is that, despite their numerous
similarities, cat species differ from one another.
"These differences are showing us how these animals are perfectly suited
for their natural environments," Murphy stated. For conservationists and
other people trying to protect or restore species in their native
environments, knowing that they are not interchangeable is important.
"For example, you can't assume that tigers from Sumatra and Siberia are the
same," he stated. "Their environments are wildly different, and those tiger
populations have likely developed specialized genetic adaptations to help
them survive in these very different places."
It's also critical for scientists to recognize that the most challenging
genomic regions to assemble could hold the key to comprehending vital
physiological processes like immunity and reproduction.
Not all genes have been difficult to sequence and investigate, including
those related to smell. Previous studies lack this sort of information since
scientists have also had difficulty sequencing genes related to immunity and
reproduction. Completing genome assemblies is important since it is
difficult to research a genetic problem in people, cats, or any other animal
without all the components "Murphy added.
For the time being, Murphy and his colleagues will keep using the most
cutting-edge genome assembly and sequencing methods on cat genomes to add as
much information as they can on the world of cats.
Wes Warren, a professor of genomics at the Bond Life Sciences Center at the
University of Missouri, and Bill Murphy, a VMBS professor of veterinary
integrative biosciences at Texas A&M, designed the project. Researchers
from Louisiana State University, the Guy Harvey Oceanographic Center, the
Institute for Systems Biology in Seattle, University College Dublin, and the
University of Washington collaborated in other projects.
