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The Tree of Life Revealed (Ruminant Division)

MU researchers find a way to rapidly reconstruct the genetic heritage of evolutionary-related animals

At first glance, the long-necked giraffe and the sturdy bison seem to have little in common. A research study at the University of Missouri is showing that these two diverse animals share a common heritage, and those genetic connections may help future scientists understand the evolution of biology and physiology of animals, develop healthier and more efficient cattle, find ancient relatives and understand human disease.

Using a new genotyping assay and a technique for preparing DNA from ancient fossil samples, MU scientists and a team of international researchers have produced genotypes that can be used to create a "tree of life" for living and extinct ruminant species. The team can go as far back as far as 29 million years and connect the heritage of species as diverse as duikers and giraffes.

The team's novel approach may transform studies of evolution and domestication through rapid and inexpensive generation of data on the evolutionary relationships among species. The research is being published in the Proceedings of the National Academy of Sciences.

"We studied 678 different animals representing 61 different species, and using the new Illumina cow single nucleotide polymorphism 'SNP chip,' we were able to generate very high quality genotypes in species for which the chip was not designed," said Jerry Taylor, the Wurdack Endowed Chair in Animal Genomics, Division of Animal Science, at the MU College of Agriculture, Food and Natural Resources and lead author of the study.

'SNP chips' allow scientists to simultaneously examine thousands or even hundreds of thousands of specific positions throughout an animal's genome to detect the DNA bases that are present at these sites.

"We were very surprised to find that the chip produced high-quality data in species that were very diverged from cows," Taylor said. "In less than a week we were able to produce five times as much information as has previously been used to construct a 'tree of life' for the ruminants."

The team also established the feasibility of high-throughput genotyping of ancient samples by genotyping replicate samples from a fossil bison bone and showing that Bison priscus and modern bison were sister species.

"Our results strongly suggest that researchers can assess the fidelity of genotypes they produce from ancient samples by examining where the species is placed in a well-resolved tree, and samples producing unreliable genotypes can be identified and removed from further analysis," Taylor said.

Also revealed, the history of domestication

"When we applied this chip to 48 recognized breeds of cattle, we were able to construct a tree based upon the extent of similarity or difference between the DNA of members of different breeds which allowed us to infer the history of cattle domestication and breed formation across the globe," Taylor said.

"We've known for some time that the humped indicine and non-humped taurine cattle represent separate domestications, but our data indicate that if there was a third domestication event for cattle it was most likely in Africa, with a fourth event in East Asia much less likely."

The work also revealed that European cattle domestication was probably influenced by migrations out of the Fertile Crescent, with domesticated cattle moved sequentially through Turkey, the Balkans and Italy, then radiating through Central Europe and France, and finally into the British Isles. Interestingly, they also found evidence supporting a second route of ancient cattle importation into Europe via the Iberian Peninsula.

A human application?

Other applications for this technology could go beyond ruminants, Taylor said. They may help solve a number of problems and answer questions about evolution, including how modern humans are related to extinct hominids and how different plant species are related to each other, Taylor said.

"It also enables informed conservation efforts, because the approach gives you both the ancestral relationships between species and the amount of diversity within a species, which are critical for the identification of species and populations within species to target for preservation."

Taylor said that based on this research, scientists can also begin to study genome evolution and the evolution of biological function from a phylogenetic (the study of evolutionary relatedness among various organisms) perspective. Taylor said.

"For example, if breeds of cattle with the propensity to accumulate high amounts of intramuscular fat, known as marbling, are closely related to each other, they are likely to share the same variation in the same genes that create that marbling," he continued. "However, if they are not closely related, different genetic variants might be at work. Understanding how different genes create variation that allows high levels of marbling, feed efficiency and disease resistance in cattle could have a large economic impact for farmers who raise cattle throughout the world."

The research may also provide opportunities to identify animal models for human disease, Taylor added. For example, the excess accumulation of intramuscular fat in humans is associated with insulin resistance and type 2 diabetes.

"We're all interested in reconstructing our ancestry," Taylor said. "This is essentially the same thing, except that we're able to zoom out by millions of years and include relatives whom are long gone. The amazing thing about this technique is that it is very fast and extremely cheap. For relatively small amounts of money, we can generate the data that will allow us to recreate millions of years of evolutionary history."

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