iScience: Genome sequencing of endangered sharks

Professor Mahmoud Shifji said: "By deciphering their entire genomes at high resolution, we can better understand the evolutionary history
of these endangered species.
"

This stunning image describes a milestone
in the science of shark conservation.
Professors Shivji, Professor Michael Stanhope and their collaborators looked back at history
by sequencing the genomes (the entire genetic blueprint) of hammerhead sharks and shortfin mako sharks.
Their DNA timeline shows that their numbers have declined
dramatically over a period of 250,000 years.
Scientists have also found something worrying: Sledgehammerhead sharks have low genetic variation, which makes them less
able to adapt to our rapidly changing world.
The species also shows signs of inbreeding, a problem that may reduce the viability
of its population.
However, shortfin mako sharks exhibit higher diversity and limited inbreeding, a ray
of hope in a bleak conservation climate.
Understanding changes over such a large timescale can shed light on the current conservation status
of these endangered animals.
The findings can help us find more nuanced shark management strategies
.

The findings, published in iScience, were led by Professor Stanhope of Cornell University and Professor Shivji, director of the Save Our Ocean Foundation Shark Research Center and the Guy Harvey Institute at Nova Southeastern University, in partnership with Cornell University, Nova Southeastern University, Temple University, Governors State University, and the San Diego Zoo Wildlife Alliance
.
The scientists obtained and assembled the entire genome sequences of the Sledgehead shark and the shortfin mako shark and compared their genomes with those of whale sharks, white sharks, brown bamboo sharks and cloud cat sharks
.
Their method reads like a scientific detective's complex puzzle: assembling small pieces of DNA of different sequences in sequence, like a giant patchwork tapestry
depicting the blueprint of life.
Reaching the chromosomal level represents the latest in high-quality whole-genome sequencing research — a tricky feat
for a species like sharks with huge genomes.

Along with the application of advanced technology, reports of sharks and rays are also bleak
.

Professor Stanhope said: "Technological advances in genomic research mean that DNA sequencing methods are now more powerful and effective
.
"We can apply these new technologies to understand this creature, and we hope to use this information to protect sharks and rays
.
"

While we don't know the exact effects of shark inbreeding, studies of wolves and cheetahs suggest that problematic traits slowly emerge
over time.
The result is often a reduction in the survival
of the species.
The situation with the Sledgehammerhead shark is worrying – overfishing and trading their fins
.
But without these key genetic insights, we won't be able to change the way
vulnerable groups are currently managed.

Researchers are wary of exaggerating the results
.

"Advances have been made in genetics, and genomes at the chromosome level are the expectation of
a species' reference quality genome.
However, conservation research presents its own challenges to achieve this consistent and anticipated solution
in other areas.
Professor Shivji added: "Access to tissue samples from endangered marine vertebrates is a major obstacle
.
You can assemble a genome from a single tissue sample of a shark, but ideally sequencing the genomes of multiple individuals from different ocean regions is ethically difficult and
costly.
”

In fact, the researchers believe this is a limitation
of their current study.
The ethical limits to studying endangered species mean that conservation geneticists must strike a balance
between recent advances and respect for the vulnerable populations they study.
In addition to revealing the genetic diversity and vulnerability of two endangered shark species, the researchers hope their results will provide what they call a reference-quality genome on which future basic science could improve our understanding
of sharks.
Of course, as new possibilities emerge, our insights into shark blueprints will help enhance our understanding of these ecologically important species and protect their vulnerable populations
.