The DNA Mystery Inside Every Great White Shark That Science Still Can't Explain

13 July 2026 | White Shark Ocean

The great white shark has been one of the most intensively studied marine predators on earth for decades. Its behaviour, physiology, genetics, and ecology have been the subject of thousands of research papers. Scientists have tagged individuals, tracked their ocean crossings, analysed their teeth, sequenced their genomes, and measured the electrical fields they produce. In many respects, the great white is one of the best-understood large animals in the ocean.

Which makes it all the more striking that a study published in the Proceedings of the National Academy of Sciences in August 2025 concluded, after analysing one of the largest great white shark genetic datasets ever assembled, with a finding that one of the study's senior authors described as follows: "The honest scientific answer is we have no idea."

Two Types of DNA, Two Completely Different Stories

To understand the mystery, it helps to know that living cells carry DNA in two separate locations. Most DNA lives in the cell nucleus — this is the genome most people think of when they think about genetics. But a separate, much smaller set of genetic instructions is housed in the mitochondria, the structures inside cells responsible for producing energy. Mitochondrial DNA is inherited exclusively through the maternal line: you get your mitochondrial DNA from your mother, who got it from her mother, and so on back in time.

For most species, nuclear DNA and mitochondrial DNA tell broadly consistent stories about a population's history and structure. They are different systems with different inheritance patterns, but the major features of a species' evolutionary history tend to show up in both. When the two tell radically different stories, something unusual is going on.

In great white sharks, the two tell radically different stories.

The nuclear DNA of great white sharks is strikingly similar across the globe. A great white from the coast of South Africa, a great white from California, and a great white from South Australia carry nuclear genomes that are far more alike than you would expect from animals separated by entire ocean basins with minimal interbreeding. By the logic of nuclear DNA alone, great white sharks look like a single, well-mixed global population that has been sharing genes relatively freely for a long time.

The mitochondrial DNA tells the opposite story. Analysed by itself, the mtDNA of great white sharks is highly divergent between regions — suggesting populations that have been reproductively separated for long enough to accumulate significant genetic differences. By this measure, great whites look like distinct regional populations with very limited exchange between them.

Both sets of data come from the same sharks. They cannot both be right in the straightforward sense. Something in the biology or history of the species has produced a mismatch that does not resolve neatly into either story.

The Hypothesis That Didn't Hold

For years, the leading explanation for the nuclear-mitochondrial mismatch was philopatry: the tendency of animals to return to the same location to breed. The theory went like this. Male great white sharks roam widely across ocean basins, mixing their nuclear genes freely across populations. Female great white sharks, by contrast, return to the same regions to pup — and since mitochondrial DNA is inherited only through the maternal line, the females' site fidelity would produce divergent mitochondrial patterns even as the males' wandering produced uniform nuclear patterns.

It was an elegant explanation, and it fit with what was known about great white behaviour. Males are the more widely ranging sex — they travel further, spend longer in open ocean, and show less consistent return to specific locations. Females, particularly pregnant females, have been observed returning to the same coastal areas across multiple years. The hypothesis was plausible, and for over two decades it was the working assumption.

The 2025 PNAS study, led by researchers at the Florida Museum of Natural History and the Florida Program for Shark Research, set out to test it properly. The team assembled one of the largest white shark genetic datasets ever collected, analysing both nuclear and mitochondrial DNA from individuals across the species' global range with enough statistical power to detect subtle signals in the data.

The test was direct: if female philopatry were driving the mitochondrial divergence, some trace of that same geographic structure should appear in the nuclear DNA — perhaps very faint, given the males' mixing, but detectable. The researchers looked for it. They found nothing. The nuclear DNA showed no geographic structure at all that would be consistent with females preferentially breeding in their home regions. Philopatry could not explain what the data showed.

"We specifically tested the sex-biased dispersal hypothesis," said Gavin Naylor, the study's senior author and director of the Florida Program for Shark Research. "And it doesn't hold up."

What the Ice Age Left Behind

The 2025 study did make one significant positive finding, even as it demolished the previous explanation. The genetic data, analysed across time, showed a clear signal: approximately 10,000 years ago, at the end of the last ice age, all great white sharks appear to have been confined to a single population in the southern Indo-Pacific Ocean. A severe population bottleneck — a dramatic reduction in the number of breeding individuals — had compressed the species into one geographically restricted group.

From that starting point, the great whites spread outward. As global temperatures rose, sea levels changed, and ocean circulation patterns shifted at the end of the ice age, the sharks gradually expanded their range across ocean basins. Today, scientists recognise three distinct genetic populations: one in the southern hemisphere spanning Australia and South Africa, one in the northern Atlantic, and one in the northern Pacific. The genetic divergence between these populations began approximately 7,000 years ago, consistent with the populations separating from the Indo-Pacific ancestor and accumulating their own mitochondrial differences in relative isolation.

This ice-age bottleneck finding has implications beyond the DNA mystery. If the entire global great white shark population was, at one point, compressed into a single Indo-Pacific group of limited size, then the species' current global genetic diversity is built on a very narrow foundation. What looks like a globally distributed apex predator was, 10,000 years ago, a geographically restricted remnant that got lucky with the end of an ice age.

Three Populations, One Unsolved Question

The three genetic populations identified in the study — southern hemisphere, north Atlantic, north Pacific — correspond broadly to what researchers had already suspected from tagging data and population estimates. The southern hemisphere population, encompassing both Australian and South African great whites, is the largest and most genetically diverse. The north Atlantic population, centred around the US east coast and the Mediterranean, is smaller. The north Pacific population, associated with the California and Guadalupe Island aggregation sites, is distinct from both.

The mystery is not which populations exist. The mystery is why their mitochondrial DNA is so divergent while their nuclear DNA is so similar — and why the most obvious explanation (female philopatry) was tested and found to be insufficient.

Several alternative explanations have been proposed. One possibility is that a historical event — perhaps the ice-age bottleneck itself — produced the mitochondrial divergence by chance, through a process called genetic drift, and that the signal has simply persisted even as nuclear genes mixed across populations through male dispersal. Another is that some form of selection is acting specifically on mitochondrial DNA in different environments, favouring different mitochondrial variants in different ocean basins in ways that maintain divergence despite nuclear mixing. A third is that there is some behavioural or ecological mechanism driving the pattern that researchers have not yet identified.

None of these explanations have been confirmed. The study's conclusion is, in the senior author's own words, that there is no consensus answer — only an acknowledged mystery that requires further investigation.

What This Means for Conservation

The practical implications of the genetic findings extend beyond academic interest. The existence of three distinct populations with limited mitochondrial exchange means that each population has its own genetic heritage. If the north Atlantic population were to be significantly reduced or eliminated, the mitochondrial lineages unique to that population would be permanently lost — they could not be replenished from the southern hemisphere or north Pacific populations with any reliability.

The ice-age bottleneck finding adds another layer of concern. A species that was already reduced to a single bottlenecked population once in its history has demonstrated that it is capable of surviving such compression — but also that the circumstances that allowed recovery (a warming climate, expanding ocean habitats, recovering prey populations) may not repeat themselves in the same way under the pressures the species faces today. The great white shark is currently listed as Vulnerable on the IUCN Red List. If the nuclear-mitochondrial mismatch eventually turns out to reflect something about the species' dispersal biology that makes population recovery harder than it looks, the conservation implications could be significant.

For now, the honest answer is that the question remains open. And in a species this well-studied, an open question this fundamental is itself a remarkable thing.

White Shark Ocean operates cage diving and surface encounters in Mossel Bay, South Africa — encounters with animals whose inner lives still hold more mystery than science has resolved. Book at whitesharkocean.com.

Frequently Asked Questions

What is the great white shark DNA mystery?

Great white sharks show a striking mismatch between two different types of genetic material. Their nuclear DNA — the main genome housed in cell nuclei — is nearly identical across individuals from different ocean basins, suggesting a single, well-mixed global population. Their mitochondrial DNA — a separate genetic system inherited only through the maternal line — is highly divergent between regional populations, suggesting long periods of reproductive separation. The two types of DNA tell opposite stories about the species' history, and a major 2025 study published in PNAS found that the most widely accepted explanation — that female site fidelity drives the pattern — does not hold up when properly tested.

Why is the great white shark DNA mismatch unusual?

For most species, nuclear and mitochondrial DNA tell broadly consistent stories about population history. When the two diverge radically, it indicates something unusual in the species' biology or history. In great white sharks, the divergence is so significant and so inconsistent with the leading explanatory hypothesis that the senior author of the 2025 PNAS study — Gavin Naylor, director of the Florida Program for Shark Research — described the honest scientific position as: "We have no idea." That kind of acknowledged uncertainty, for one of the most studied marine species in the world, is genuinely unusual.

What did the 2025 great white shark genetics study find?

The study, published in Proceedings of the National Academy of Sciences in August 2025, used one of the largest white shark DNA datasets ever assembled to test the hypothesis that female philopatry (returning to the same place to breed) could explain the nuclear-mitochondrial mismatch. The test found no evidence in the nuclear DNA consistent with this hypothesis. The study also confirmed that approximately 10,000 years ago, at the end of the last ice age, all great white sharks were compressed into a single Indo-Pacific population before expanding globally — and that three distinct genetic populations (southern hemisphere, north Atlantic, north Pacific) have been diverging for approximately 7,000 years.

How many great white sharks are there in the world?

Population estimates for great white sharks are difficult to produce reliably because the species is widely distributed, spends significant time in open ocean, and aggregates at specific sites only seasonally. Current estimates suggest a global population in the range of 3,000 to 5,000 individuals, though some regional estimates are considerably lower. The 2025 genetics study is consistent with this picture of a globally restricted species whose total diversity rests on a narrow genetic foundation — the product of an ice-age bottleneck that compressed the entire species into a single small population before the current distribution developed.

Are great white sharks endangered?

Great white sharks are currently listed as Vulnerable on the IUCN Red List. Some regional populations are under considerably more pressure than the global listing suggests: Australia's breeding population was estimated in a 2025 DNA study at fewer than 500 individuals, and several other regional populations face ongoing mortality from shark nets, bycatch, and targeted fishing. The genetic findings from the 2025 PNAS study — particularly the evidence of the ice-age bottleneck and the distinct population structure — underscore the conservation importance of each regional population as a separate genetic unit that cannot easily be replaced from elsewhere.