Scientists have sequenced the chromosome-level genomes of the great hammerhead (Sphyrna mokarran) and the shortfin mako (Isurus oxyrinchus) sharks. Their results show that both these sharks experienced precipitous declines in effective population size over the last 250,000 years.
The great hammerhead shark (Sphyrna mokarran). Image credit: Christopher Vaughn-Jones.
The class Chondrichthyes (sharks, rays, and chimeras) has a history that dates back about 420 million years over which time it has survived five mass extinctions.
Today this ancient lineage finds itself in a new geological epoch — the Anthropocene, which may well be characterized as the sixth mass extinction.
In a recent report by the IUCN Red List of Threatened Species, 31% of all shark species are threatened, a figure considerably higher than their 2014 estimate. Of these threatened shark species, 6.5% are critically endangered and 10.5% are endangered.
Another recent report indicates the global abundance of oceanic sharks and rays has declined by 71%, due to an 18-fold increase in relative fishing pressure.
In 1980, only 9 species of oceanic sharks and rays were threatened on the IUCN Red List category, but in 2021, 75% of these species are now threatened.
The great hammerhead and the shortfin mako sharks are two examples of this recent dramatic decline in this group.
The great hammerhead is the largest species of hammerhead shark in the family Sphyrnidae reaching a maximum size of about 6 m.
The species has a worldwide distribution, found in coastal tropical and warm temperate seas.
It has a wide ‘hammer’ (cephalofoil), tall sickle-shaped dorsal fin, and is an important apex predator.
Its critically endangered status is primarily due to heavy fishing for its large fins, which are highly valued in the shark fin trade.
The shortfin mako is a predominately pelagic, apex predator, reaching a maximum size of about 4 m, and is found worldwide in temperate and tropical seas.
It is classified within the family Lamnidae which includes all of the known partially endothermic sharks.
The endangered status of the species is primarily due to commercial and sport overfishing.
The shortfin mako shark (Isurus oxyrinchus). Image credit: Simon Hilbourne.
“With their whole genomes deciphered at high resolution we have a much better window into the evolutionary history of these endangered species,” said Professor Mahmood Shivji, a researcher at Nova Southeastern University and director of the Save Our Seas Foundation Shark Research Center and the Nova Southeastern University’s Guy Harvey Research Institute.
“Their DNA timeline shows that their populations have declined substantially over 250,000 years.”
Professor Shivji and colleagues acquired and assembled entire genome sequences for great hammerhead and shortfin mako sharks and compared their genomes with genome information available for the whale shark, white shark, brownbanded bamboo shark and cloudy catshark.
Their methods read like complex puzzle-building by scientific sleuths: successively assembling from tiny fragments of DNA different sequences like a great patchwork tapestry that details the blueprint of life.
Reaching chromosome level represents the latest in high-quality whole genome sequence research — and a tricky feat to achieve for species like sharks that have enormous genomes.
The authors found that great hammerhead sharks have a high probability of inheriting two copies of the same DNA sequence (homozygosity), including various genes, from their parents.
“To understand why this might be undesirable, you can think about it in terms of disease,” Professor Shivji said.
“You need two copies of the gene to express certain recessive diseases: one from your mother and one from your father.”
“If you are homozygous for a trait, you have inherited the same gene sequence from both your mother and father, and the trait will be expressed.”
In the case of great hammerhead sharks, showing what the scientists dub ‘high runs of homozygosity’ in their genome means that large sections of their genome were homozygous, increasing the chances of expressing undesirable traits.
By contrast, if one inherits two different sequence forms (alleles) of a gene from the mother and the father (i.e., heterozygosity), the effects of the recessive allele can be masked by the dominant allele.
If an undesirable trait is recessive in this heterozygous state, it will not be expressed.
Shortfin mako sharks had lower runs of homozygosity relative to great hammerheads, a genetic windfall that may stand them in better stead to adapt to change.
The application of advancing techniques comes amidst bleak reports for sharks and rays.
“Technical advances in the study of genomes mean that DNA sequencing approaches are much more powerful and efficient now,” said Dr. Michael Stanhope, a reseacher at Cornell University.
“We can apply these new technologies to gain insights about the organism, information that we hope can be leveraged to protect sharks and rays.”
“While we don’t know exactly the effects of inbreeding in sharks, findings from wolves and cheetahs show that problematic traits can creep in over time. The result is often lowered survival of the species.”
“The picture for great hammerhead sharks — overfished and traded for their fins — is worrying.”
“But without these critical genetic insights, we would be unable to modify how their vulnerable populations are currently managed.”
The team’s results were published in the journal iScience.
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Michael J. Stanhope et al. 2023. Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead. iScience 26 (1): 105815; doi: 10.1016/j.isci.2022.105815
