What scientists learned about whale sharks from the DNA they left behind in seawater


Whale sharks are the largest fish in the ocean, but that doesn’t mean they’re easy to study. Scientists hoping to learn about them must spy on them from the air, tag them with devices so they can be tracked via satellite or sneak up on them to collect tissue samples for DNA analysis.

But there may be an easier way.

Researchers from Denmark and Qatar were able to learn about a group of whale sharks in the Persian Gulf simply by gathering the seawater around them and analyzing the “environmental DNA” it contained.

With 20 samples of seawater, the research team was able to show that the recently discovered group of about 200 whale sharks were more closely related to whale sharks from the tropical portions of the Indian and Pacific oceans than to the colonies in the Atlantic. They were also able to estimate the number of breeding females in the population, according to a report published Monday in Nature Ecology & Evolution.


The surface seawater samples were collected from 15 spots around the Al Shaheen oil field, where the whale sharks had been observed. Most of the samples contained just 1.5 liters of water.

The researchers used DNA sequencing machines to decode the mitochondrial DNA extracted from the water. Mitochondrial DNA is found in the part of the cell that converts food into energy, and it’s passed down from mother to child virtually unchanged.

By zeroing in on a few sections of the mitochondrial genome, they were able to gauge the genetic diversity of the Persian Gulf whale sharks and compare them to their cousins in the Atlantic, Indian and Pacific oceans.

The team was able to check its work because it also had access to mitochondrial DNA from tissue samples collected from 61 whale sharks who swam in the same waters. The genetic fingerprints — collections of mutations known as haplotypes — were found in similar frequencies in both the seawater samples and the whale shark tissue, according to the study. What’s more, the catalog of haplotypes gathered from the seawater was more complete than the ones contained in the tissue samples alone.

By counting up the accumulated mutations in certain parts of the genome, the researchers calculated that the whale sharks had an “effective female population size” of between 43,618 and 183,526. (This is the population of mothers that give birth to the next generation.) Doing the same analysis with the tissue samples instead of the DNA from seawater yielded a range of 85,087 to 351,654 females.

Although the average of the two ranges were off by nearly a factor of two (71,600 versus 138,400), the fact that they overlapped at all shows that environmental DNA offers a “promising” way to estimate effective population size, the researchers wrote.

The seawater samples also contained DNA fragments from mackerel tuna, which spawn near Al Shaheen. In fact, the greater the concentration of whale shark DNA, the greater the concentration tuna DNA. The reverse was also true — when whale shark DNA was relatively scarce, tuna DNA was scarce as well. This is “most probably” a sign that the whale sharks had come to the area to feed on tuna spawn, the researchers wrote. (It’s also possible that the tuna were following the whale sharks, though “this has never been observed in Al Shaheen,” they noted.)

Other groups have already used environmental DNA to identify the inhabitants of certain waters, but this is the first study to show that environmental DNA can provide meaningful information about a population of animals and the biodiversity of their habitat, the authors wrote.

Follow me on Twitter @LATkarenkaplan and “like” Los Angeles Times Science & Health on Facebook.


Scientists aim to feed the world by boosting photosynthesis

By drawing 50 ‘states’ according to income, study reveals ‘developing countries’ within the U.S.

Pluto has a cold, wandering heart, and maybe a hidden ocean too


Nov. 23, 8:35 p.m.: The story has been updated to include additional details from the study.

The story was originally published at 6:10 p.m. on Nov. 21.