Here’s why a SA researcher is DNA barcoding fish larvae

It’s spawning season and approximately 1 million fish eggs have just been released into the surf near Cape Padrone on the South East coast of South Africa.

After a few days, the first egg hatches – larvae need to fend for themselves amid countless sea predators.

After a month the 1cm larva picks up chemical signals of freshwater from the Sundays River estuary and begins to “smell” its way to the upper reaches, eventually emerging as an “early juvenile”.

 

‘Sad story’

Much like kindergarten, the estuary is supposed to be a safe haven for one of South Africa’s most prized fish, the dusky kob.

The juvenile will outgrow its nursery phase and move into the open sea after about 2-3 years.

Dusky kob is the perfect example of a fish that requires an estuary to complete its lifecycle. Bagging dusky kob (Aka kabeljou) is many an angler’s dream.

Unfortunately, this dream has become the kabeljou population’s nightmare.

Fish expert JD Filmalter told The Mission Fly Mag, a fly fishing magazine, that “the story of the dusky kob is actually quite sad: …almost 20 years ago a population estimate based on declining catch rates put the number of breeding adults at less than 5% of their historic unfished levels”.

The dusky kob is currently listed as Endangered by the International Union for Conservation of Nature (IUCN) and represents one example of a local fish population that is suffering. There are likely to be many more.

One of the biggest challenges in the conservation of fish species like the dusky kob is the identification at the larval stage of development.

 

‘Hours to years’

 

In 2016 marine larval connectivity expert, Prof Francesca Porri from the South African Institute for Aquatic Biodiversity (SAIAB), received a SANBI Foundational Biodiversity Information Programme (FBIP) Small Grant to look at the challenge of identifying invertebrate and fish larval stages for coastal species.

Once the fish (or marine invertebrate) eggs hatch, the larval stages are dispersed in the water column for periods that can range from hours to years.

“The supply of larvae plays a key role in maintaining the stability of adult populations of coastal species.

And being able to resolve the taxonomy of early larval stages is important in understanding the ecological drivers of coastal dynamics.

Using traditional morphological methods to identify marine larvae is a shot in the dark as most of these larvae do not resemble their adult counterparts, making taxonomic identification difficult,” said Prof Porri.

To overcome this challenge Prof Porri and her team turned to hi-tech DNA barcoding.

DNA barcoding involves meticulous laboratory protocols – it focuses on a certain gene region in the animal’s DNA, and like a cashier’s checkout scanner kicks out a highly unique sequence of “ACGT’s” for every species.

 

Filling the gap

Many of the larval taxa targeted for DNA barcoding in Prof Porri’s project belong to commercial fish species.

This adds value to the study with potential links to the management of marine resources.

This is important from a marine protected areas perspective, for which successful identification of larval specimens and scales of ecological connectivity are ultimate goals.

Prof Porri, a National Research Foundation (NRF) rated “established” researcher, says that while DNA barcoding libraries are increasingly able to ID the adults of South African coastal invertebrates and fish, molecular validation for larvae is still largely overlooked, leaving a large and important gap.

“This project, therefore, gave us the opportunity to fill (or start filling) such a gap, with the larval stages of about 30 species (between invertebrates and fish) being successfully barcoded (forward and reverse sequences),” she told the FBIP.

 

Science to society

As a recipient of a Small Grant Prof Porri’s project needs to contribute to the FBIP themes of Global Change and the Bioeconomy.

She says that being able to accurately resolve the taxonomy of early life stages of marine species is of key relevance to addressing the impact of climate change on early life stages.

Populations bottlenecks, where a random event – e.g., environmental disaster – can wipe out the genetic diversity of a population, often hit the most vulnerable phase of a marine organism, especially in terms of physiology.

Foundational knowledge on the identity of these larvae will help generate a reliable understanding of where early life stages of many marine species can live, survive or define the environmental ranges of occurrence.

Similarly, the identity of early stages will also establish real links to their adult counterparts, some of which are consumed by humans and are hence applicable to the management/conservation practices.

This generated knowledge can therefore ultimately further add value to foundational research and help better connect this domain of science to society.

 

Unique product

Prof Porri’s work takes foundational biodiversity science to new heights through the creation of a DNA barcoding library, matched by photographic evidence and morphological confirmation of about 30 coastal taxa – these are currently being revised for a manuscript.

“This output will be the first of its kind for South Africa and a unique product that will improve the correct identification of the early stages of coastal species. It will therefore help link the ecology and management of adult species,” said Prof Porri.

The project also developed two MSc students, who were afforded the opportunity to acquire molecular expertise in DNA barcoding of marine larvae.

A post-doctoral fellow associated with the project provided guidance and training.

For Prof Porri and her team, this project was a small step in the direction of cataloging the diversity of the larval stage of fish like the endangered dusky kob.

This type of information forms the basis for the conservation of many economically important marine species.