Past to Future: breakthrough as great hammerhead and shortfin mako genomes sequenced

Tiny fragments of DNA. That’s where this 250,000-year-old story begins for two endangered shark species. The speed and agility of a hunter like the shortfin mako, the mystery and nomadism of the great hammerhead shark isolated into small pieces that read like hints and clues to those versed in their code. After the DNA is extracted from the organ tissue of great hammerhead and shortfin mako sharks, a complex sequence of scientific sleuthing unfolds. Piece by piece, conservation geneticists assemble the genome (the entire set of genetic material in an animal) for these enigmatic creatures about which we still have much to learn. In the end, a blueprint for life is formed like some molecular patchwork quilt. And it is from this lab-level puzzle-building that alarm bells are now ringing for the great hammerhead, whereas we might glean some slim hope for the shortfin mako shark.

Scientists have sequenced to chromosome level, for the very first time, the entire genome of the Critically Endangered great hammerhead shark and the Endangered shortfin mako shark. Their findings raise red flags for the management of great hammerheads: low genetic diversity and signs of inbreeding come as insights that add a blow to populations already in free fall due to overfishing. With a larger historical effective population size (the ideal breeding population size), the shortfin mako shark shows higher genetic diversity that may make these sharks more resilient to ongoing environmental change, but only if the current fishing pressure on them is reduced. The populations of both shark species, the scientists showed, have suffered major declines over 250,000 years. While that might not seem applicable to current conservation, it is only by looking at the demographics (population trends) and conservation genetic measures in the context of their entire evolutionary history that we can holistically manage their populations today.

Shortfin mako sharks showed higher diversity and limited inbreeding, a hopeful glint in the gloomy conservation climate. Photo © Simon Hilbourne

The findings come from a new scientific paper published in iScience and titled ‘Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead’, led by Professor Michael Stanhope from Cornell University and Professor Mahmood Shivji, director of the Save Our Seas Foundation Shark Research Center and Guy Harvey Research Institute, based at Nova Southeastern University, working with collaborators from Cornell University, Nova Southeastern University, Temple University, Governors State University, and the San Diego Zoo Wildlife Alliance.  The scientists acquired and assembled entire genome sequences for great hammerhead and shortfin mako sharks to highlight their population histories and to decipher the information about their genome-level diversity that is needed for their conservation. They compared their genomes with genome information available for the whale shark, white shark, brownbanded bamboo shark and cloudy catshark.

Why conservation genomics?

‘There is a handful of groups around the world that are dedicated to sequencing the genomes of a variety – if not all – living beings,’ explains Professor Shivji. ‘This push to gain genetic insights across a wide range of life on earth has been sparked by the successes of the Human Genome Project, which was based on the best technology at the time (about 22 years ago).’ The project, which helped uncover historical human migration patterns and gave us a human ‘blueprint’, resulted in a major leap forward for medicine and the study of human biology. ‘Technical advances in genomics mean that DNA sequencing approaches and related computational bioinformatics analyses are even more powerful and efficient now”, says Professor Stanhope. ‘We can apply these new technologies to gain biological insights about marine species, information that we hope can be leveraged to protect sharks and rays’.

The application of advancing techniques comes amid reports that paint a bleak picture for sharks and rays. One-third of all sharks and rays are threatened with extinction, according to the latest International Union for the Conservation of Nature (IUCN) Red List updates. It is a situation that is primarily the result of overfishing and is compounded by climate change and pollution. Managing and conserving sharks is no straightforward business; every layer of insight helps broaden our understanding of their biology, the threats they face, how they might respond to certain pressures and what solutions would be the best fit for each species. Conservation genomics is another tool in the arsenal of concerned scientists that adds a molecular – and now an evolutionary – perspective to a complex picture. ‘Having entire shark genomes deciphered at high resolution provides a much better view of the evolutionary history of these enigmatic species,’ reflects Professor Shivji, as we discuss how the 250,000-year timeframe broadens our very concept of what these sharks are. It’s certainly a perspective that cannot be gained from fisheries biology or ecology alone.

Reaching chromosome level represents the latest in high quality genetic research, a tricky feat for sharks that have large genomes. Photo © Chris Vaughan-Jones

Why chromosome-level genome sequences?

Genetics has advanced such that chromosomal level (very high-resolution) genomes are the expectation for a reference quality genome for species. However, achieving this level is a tricky feat for species like sharks that have large genomes compared to most vertebrates. ‘Conservation research presents its own challenges to achieving this consistently and at the resolution expected in other fields’, says Professor Shivji. Ethically obtaining tissue samples from endangered species is a major hurdle. In the case of this study, tissue from the heart of a single shortfin mako male and a single great hammerhead female were obtained by recreational fishers. Professor Shivji points out the caveat in the research: that the findings come from the genomes of a single animal to avoid going out to lethally sample more specimens.

‘You can assemble the genome 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,’ he explains. ‘But these samples also need to be fresh; they can’t come from catches of fishers that may have been sitting for a few hours or days.’ Lethal sampling from already waning populations raises serious questions. Professor Shivji points out that the current ethical limitations to working with endangered species may, in time, lead to alternative non-lethal routes that don’t risk damaging the very shark populations they seek to conserve. In the interim, achieving chromosome-level genome sequencing means that the field of conservation genomics must balance forging ahead with the latest advances with a mindfulness that respects the fragile populations they seek to understand.

What does low diversity mean for sharks?

Genetic diversity is the biological foundation for most species to be able to adapt to and survive changes in the environment. What the researchers found in this study is worrying for great hammerhead but hopeful for shortfin mako: the great hammerhead shark has notably low genetic variation, which means that it is less resilient to adapting to our rapidly changing oceans. Equally concerning was the finding that the species also shows signs of inbreeding, an issue that can lower the ability of its populations to survive. While we don’t know exactly the effects of inbreeding in sharks, findings from other species such as wolves and cheetahs show that strange and often problematic traits can creep in over time. The result is often lowered potential for the survival of the species. But the shortfin mako shark showed much higher diversity, a hopeful glint in the gloomy conservation climate.

The concern for great hammerhead sharks lies in the finding that they 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,’ explains Professor Shivji. ‘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 environmental change.