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Scientists Sequence The Genomes Of Endangered Sharks

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“With their whole genomes deciphered at high resolution we have a much better window into the evolutionary history of these endangered species,” says Dr. Mahmood Shivji, professor of marine science at Nova Southeastern University's (NSU) Oceanographic Center in Florida and director of the Save Our Seas Foundation Shark Research Center and Guy Harvey Research Institute. Shivji, along with Dr. Michael Stanhope from Cornell University, and numerous other collaborators have been able to peek back in shark-history thanks to genome sequencing, a scientific method that is used to determine the entire genetic makeup of a specific organism or cell type.

Led by Professor Stanhope, the findings of this latest scientific endeavor are published in a paper in iScience. Driven by wanting to uncover the mysteries of the past for sharks, the scientists were able to sequence to chromosome level the genomes to look at the entire genetic blueprint of great hammerhead and shortfin mako sharks. The great hammerhead shark (Sphyrna mokarran) is the largest of modern hammerhead species while the shortfin mako shark (Isurus oxyrinchus) is famous for their speed and agility. These hammerhead sharks have a circumglobal distribution in tropical and warm temperate seas, and shortfin mako sharks are also found in all tropical and temperate seas. Both predators face mounting pressure from fisheries worldwide, and are regularly taken as bycatch or intentionally targeted for their fins. We’re at a critical point for these predators, which is why the team was especially focused on them.

“Conservation genomics is a field increasing in importance with the continuous improvement in sequencing technologies that afford the ability to assemble high quality reference genomes,” the authors explain in their paper. “From such single genomes, it is possible to derive estimates of heterozygosity, inbreeding, and demographic history.” So, the scientists acquired and assembled entire genome sequences for great hammerhead and shortfin mako sharks and compared their genomes with the genome information available for other sharks - specifically the whale shark (Rhincodon typus), white shark (Carcharodon carcharias), brownbanded bamboo shark (Chiloscyllium punctatum), and cloudy catshark (Scyliorhinus torazame). Seems easy enough, but reaching chromosome level is not a simple feat - especially for species like sharks that have enormous genomes!

“Technical advances in the study of genomes mean that DNA sequencing approaches are much more powerful and efficient now,” says Professor Stanhope. “We can apply these new technologies to gain insights about the organism, information that we hope can be leveraged to protect sharks and rays.” A lot of hard work, similar to detectives slowly piecing together a crime scene from small clues. But it paid off: their DNA timeline shows that their populations have declined substantially over the last 250,000 years. Not only that, but great hammerhead sharks revealed a low genetic variation, which makes them less resilient to adapting to our rapidly changing world. Low genetic variation means there is signs of inbreeding, an issue that can lower the ability of its populations to survive. While we don’t know how this will impact sharks (as there are limited studies of the effects of inbreeding in sharks), we can see from other animals that it can lead to problematic traits. “Without these critical genetic insights, we would be unable to modify how their vulnerable populations are currently managed,” the researchers stated.

But while the news was worrying for hammerheads, there was a bright spot for shortfin mako shark, which showed higher diversity and limited inbreeding, a hopeful glint in the gloomy conservation climate. Understanding change over such a large timescale can put into context the current conservation status of these endangered animals. The results can help direct us towards much more nuanced management strategies for sharks. “Our hope is that the reference quality genome sequences presented here will provide a foundation for further basic research and genetic management of these endangered marine apex predators,” the authors concluded in their paper.

They do, however, want to be cautious about overstating results. “Genetics has advanced such that chromosomal level genomes are the expectation for a reference quality genome for species. However, conservation research presents its own challenges to achieving this consistently and at the resolution expected in other fields,” says Shivji. “Obtaining tissue samples from endangered marine vertebrates is a major hurdle. You can assemble the genome with a single tissue sample from a single shark, but the ideal circumstance would be to sequence genomes from multiple individuals from different parts of their ocean range, an ethically difficult and costly endeavour.”

Indeed, the researchers state this as a limitation of their current study. The ethical limitations to working with endangered species means that conservation geneticists must balance the latest advances with respect for the fragile populations they study. But as new possibilities arise, these insights into the blueprint of sharks will help strengthen the way we understand these ecologically important species and conserve their vulnerable populations.

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