A Genetic Bug Remaining in the King of the Sea? The Unsolved Mystery of Great White Shark DNA - The Inexplicable Divergence in Apex Predators that Survived the Ice Age

“The Double Genetic Story” Gets Even Stranger

There is no marine predator as famous as the great white shark, yet its genetic history remains one of the world's most perplexing mysteries. A new review article by IFLScience introduces the latest research that tentatively challenges long-held beliefs, concluding with the researchers' words: "The conclusion is 'we don't know'." At the heart of the issue is the "double story" where nuclear DNA is remarkably similar across regions, while mitochondrial DNA (mtDNA) varies significantly by region. 

Bottleneck from the Ice Age and the Formation of Three Populations

The research team used extensive data, including nuclear genomes and maternal genetic loci, to reconstruct past population dynamics. They found that around 10,000 years ago, at the end of the last Ice Age, great white sharks had contracted into a single, well-mixed population near a "marine enclosure" in the southern Indo-Pacific, and differentiation resumed about 7,000 years ago, leading to the current three genetic populations (Southern Hemisphere, North Atlantic, North Pacific). The total population is only about 20,000 worldwide. Florida Museum

This reconstruction aligns with the geological fact that glaciers trapped seawater, lowering sea levels by about 40 meters. As the ice melted and resources like seals became abundant in the north, it is estimated that great white sharks expanded again. Florida Museum

Re-evaluating the 20-Year-Old "Females Return, Males Roam" Hypothesis

A classic study starting in 2001 proposed that "females return to almost the same breeding sites each year (philopatry), causing regional mtDNA divergence, while males roam widely, homogenizing nuclear DNA," which became the prevailing theory. However, this time, no "traces of return" were found on the nuclear side, and even simulations incorporating the rate of mtDNA differentiation could not account for the observed differences. In other words, this hypothesis alone cannot explain the phenomenon. Florida Museum

"Brutally Lethal" Selection? The Continuing Dead End

What then caused mtDNA alone to diverge so strongly? Genetic drift, which occurs more readily in small populations, does not selectively affect only mitochondria without appearing in nuclear DNA, so it was dismissed. Natural selection remains a candidate, but the research team states that to produce such large differences in mtDNA alone in small populations would require "brutally lethal" selection. There is no definitive evidence at present, and "the honest answer is, we don't know"—this is the latest scientific conclusion. Florida Museum

Basic Knowledge: What's the Difference Between Nuclear DNA and mtDNA?

Nuclear DNA is inherited from both parents and carries most of the "blueprint" for the body's form and behavior. In contrast, mtDNA is maternally inherited in many animals and is closely related to cellular energy metabolism. The possibility that mtDNA mutations subtly adapt to environmental factors such as water temperature, movement patterns, and food resources has long been debated, but the combination of "homogeneous nuclear DNA and extremely heterogeneous mitochondria" in great white sharks remains difficult to explain. PNAS

Primary Information on the Research in PNAS

The peer-reviewed paper on this research is published in PNAS, directly testing the female-biased dispersal (philopatry) hypothesis on a genomic scale. Additionally, the research news from the Florida Museum of Natural History succinctly summarizes the recovery process from the Ice Age bottleneck and the points of denial or reservation of the prevailing theory. Readers interested in more details should refer to both sources. PNASFlorida Museum

Why the "Mystery" Matters

The genetic structure of apex predators can serve as an indicator of the stability and resilience of entire ecosystems. The fact that **the population is small (about 20,000)** suggests that climate change and prey relocation could amplify their impact. The results of this study have specifically illuminated the direction for the next experiments and observations, such as **sampling design (where, when, and from which gender)** and functional analysis of energy metabolism genes, as well as estimating selection pressures across temperature gradients. Florida Museum

Media and Social Media Reactions

This "mysterious conclusion" quickly spread across various media. Outlets like ScienceAlert, Discover, and Interesting Engineering highlighted the key points, with headlines focusing on the "testing of the prevailing theory" and the comment "we have no idea." ScienceAlertDiscover MagazineInteresting Engineering

The research body, the Florida Museum of Natural History, posted on X (formerly Twitter) that **"researchers are baffled by the strange difference between nuclear and mitochondrial DNA."** Similar announcements were made on Facebook and Threads, with a wide range of reactions in the comments, from scientific opinions like "this might rewrite textbooks" and "more samples might reveal something" to associations like "is it related to global warming or human pressure?" X (formerly Twitter)FacebookThreads

Meanwhile, the original article by IFLScience neatly organized the history of recovery from the Ice Age and the current distribution of the three populations, along with the re-evaluation of the prevailing theory. Reader comments included voices appreciating the scientific stance of honestly acknowledging "unknowns." IFLScience

Next Steps: Hypotheses to Be Tested

• Scrutinizing the Environmental Selection Hypothesis: Re-evaluate the correlation between nonsynonymous substitutions in metabolic pathways involving mtDNA (Complexes I-V) and water temperature/swimming patterns using population genomics. PNAS

• Time-Series Sampling of Gender and Age Composition: To eliminate candidates for why philopatry leaves no trace on the nuclear side, design analyses separating adults and juveniles. Florida Museum

• Expanding Wide-Range Specimens: Focus sampling on boundary areas (corridors where mixing may occur) in the North Pacific, North Atlantic, and Southern Hemisphere. Florida Museum

Conclusion—"We Don't Know" as a Starting Point

Science sometimes offers "we don't know" as the most intriguing answer. The "double genetic story" of the great white shark is a prime example of how testing prevailing theories can lead to deepening mysteries. The next steps will likely involve empirical evidence connecting function, environment, and history. The more unsolvable the mystery, the more research progresses. PNASFlorida Museum

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