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A genetic map of the reef fish in the Gulf of Eilat

A new method for identifying fingerlings using genetic coding will allow monitoring the health of the reef ecosystem in the Gulf of Eilat

Caesar fish of the generation. Not at all similar to the tiny minnow that was at the beginning of the journey. Photo: zsispeo.
Caesar fish of the generation. Not at all similar to the tiny minnow that was at the beginning of the journey. Photo: zsispeo.

The vast majority of coral reef fish, as varied and colorful as they are in adulthood, begin their lives as tiny, colorless, tadpole-like fry. When it comes to minnows, even experts can hardly tell the difference between the different species, a fact that presents a difficult challenge to reef ecology researchers. Prof. Rotem whistles from the Weizmann Institute, Prof. Roy Holtzman from Tel Aviv University, and Dr Moshe is double Ben-Gurion University in the Negev developed a new way to accurately identify fry in the water around the reef. Their research, which included genetic coding of most of the fish species in the gulf between Eilat and Aqaba, showed not only which species of fry are found in the waters of the gulf, but also how many individuals there are of each species, at what times of the year, and at what depths. This study was published today in the scientific journal Nature Ecology and Evolution.

"The ability to identify the young fry and understand their distribution in the water is very important for several reasons," says Prof. Holtzman from the School of Zoology and the Steinhardt Museum of Nature at Tel Aviv University. "First, while adult reef fish tend to stay close to their home reef, fry disperse and are carried by water currents. For marine ecologists interested in monitoring the reef, the young fry are not only an integral part of the ecosystem - they are also its future. Since the number of fry may teach us what the adult fish population will look like in the future, their monitoring may also be used in fisheries management."

Prof. Holtzman and Dr. Kafloy - both resident scientists at the Interuniversity Institute for Marine Sciences in Eilat - used the research ship of the Interuniversity Institute, which is equipped with sophisticated equipment, to sample fry at fixed depths. They sampled the fry twice a month for a year at different sites and depths near both shores of the narrow bay, as well as in its deep center. "We sampled more than 10,000 fingerlings," says Dr. Kafloy, "but the existing methods for characterizing them involve examinations under a microscope that take a long time, and can only indicate the taxonomic family, but not the species. Fortunately, we discussed this with Prof. Sorek, who happened to be visiting the inter-university institute at the same time."

Sorek's laboratory in the molecular genetics department of the Weizmann Institute usually deals with other genomes - of bacteria. "I thought that the genetic research methods we use in my lab to study bacteria might determine the identity of the fry by sequencing a 'barcode' from their genome." To this end, Omer Zuckert, a research student from Shurk's laboratory, and Dr. Gil Amitai and Sarah Melamed, faculty scientists in the same laboratory, along with Naama Kimmerling, a research student in Dr. Kafaloi's laboratory, and Tamara Gurevich, a faculty scientist in Prof. Holtzman's laboratory, carried out , as well as members of the research groups and other colleagues, adjustments in these methods for the purpose of identifying the tiny fry.

The reef minnows are so tiny that it is almost impossible to tell the different species apart. Source: Weizmann Institute magazine.
The reef minnows are so tiny that it is almost impossible to tell the different species apart. Source: Weizmann Institute magazine.

"But before we could implement the method," Sorek says, "we had to create a database of 'barcodes' for all the reef fish in the gulf. This was an operation in itself: team members dived into the bay to sample the fins of adult fish for DNA analysis. In the end, we managed to create a database of barcodes for about 80% of the main fish species known in the reef (420 out of about 540). Genetic barcode coding is based on comparing the DNA of a particular gene whose sequence is different in each species. This 'tagging' method has many applications in the world of biological research, and it was a very accurate way of matching the fry with their mature forms."

"Team members dived in the bay to sample fins from mature fish for DNA analysis. In the end, we managed to create a database of barcodes for about 80% of the main fish species known in the reef (420 out of about 540)" 

The genome sequencing of the young fish was carried out at the advanced research facilities of the Stephen and Nancy Grand Israeli National Center for Personalized Medicine at the Weizmann Institute. So far there has been no practical barcode analysis of samples containing large numbers of fry. But in this study, the entire DNA in each sample is sequenced together - whether it contained one individual or 500 individuals - using a metagenomic method. "We invented a 'trick' that makes a match between the image of the minnow and its DNA sequence," says Prof. Sorek, "which allowed us to find out exactly how many minnows of each species were in the sample. But to get one such match for each species, we had to sequence trillions of DNA bases."

In total, the research team sequenced the genomes of 10,000 minnows from 400 different samples. Thanks to this, at the end of the process, they were able to create a sort of map that showed them, for each and every species, how many details could be found, at what time of year, at what exact location and at what depth. "Since we can now analyze thousands of fingerlings with infinitely better resolution than in the past," says Dr. Kaploi, "we can focus on the ecological differences between species. If in the past we assumed that a certain taxonomic family lived in both shallow and deep water, now we see that some fish species in the family prefer the shallow water, while the others prefer deeper water - a difference that can affect their survival and distribution."

Collecting the minnows in the Gulf of Eilat using special filters. Source: Weizmann Institute magazine.
Collecting the minnows in the Gulf of Eilat using special filters. Source: Weizmann Institute magazine.

The findings also solved some mysteries; For example, the invasion of the Tylerius Spinosissimus, a small ray-finned fish from the Pufferfish family, into the Mediterranean Sea. The adult fish lives at depths of hundreds of meters, but studies have revealed that it probably invaded the Mediterranean Sea through the Suez Canal, which is only about 25 meters deep. The current study shows that the young fry of this species can live in shallow water, and are probably the ones that passed along the maritime traffic routes. The sampling also brought up fry of fish that live in a more southern area in the Red Sea, but have not yet been observed in the Gulf of Eilat. This finding raises new questions about the ecological reasons why these fish do not reach maturity in the Gulf.

Prof. Sorek concludes: "Although the initial process was a bit arduous, we now have an excellent tool for monitoring the health of the reef's ecosystem, and other reef researchers will probably use the innovative methods we developed for this research a lot in the future."

See more on the subject on the science website:

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