A winning expression of gene expression

Acclaimed talk at this year’s ASC tells the story of the genetic and phenotypic impact of size-selective harvesting on a fish stock and how underlying molecular workings drive the phenomenon of fisheries-induced evolution.
Published: 4 November 2016
​​​​​​​​​​​​​​​​Shifting characteristics

From body size to growth rate, individual fish display a range of physical characteristics – collectively known as a phenotype – which occur as a result of the interaction of a fish's genetic constitution (genotype) with the marine environment it lives in. The selection of fish acting on these phenotypic traits can result in changes across whole fish populations; for example the removal of older or larger fish favours their smaller, early-maturing counterparts, which are able to reproduce before being captured. Under this scenario, the population would genetically shift over time towards smaller fish which reach maturity at an earlier stage. This is fisheries-induced evolution in action.

Fisheries-induced evolution can be used to explain many of the phenotypic changes that have been observed by scientists, many of which remain in the population even in cases where fishing has stopped. The process is, however, difficult to both study in nature and detect signals for.

Sizing up selective harvesting

The subject was taken up by Finnish researcher Silva Uusi-Heikkilä of the Division of Genetics and Physiology at Finland's University of Turku who, together with her team, set out to look at the processes underlying fisheries-induced evolution through sequencing the transcriptome of her study species, wild zebrafish. Uusi-Heikkilä delivered her findings as part of Theme Session C at the 2016 Annual Science Conference in the Latvian capital Riga. The talk, 'The molecular mechanisms of fisheries-induced evolution', went on to win the Best Presentation Award.

One question the team sought answers to was how the selection of large individual zebrafish, as is the case in fisheries, affected the gene expression. The test was run over eleven successive generations: five for harvesting by body size and six to monitor recovery after harvesting stopped. The results showed that substantial phenotypic and genetic changes had taken place.

"After five generations we saw differences in body size, maximum body size, growth rate, energy allocation, and reproductive output (smaller fish produced fewer eggs and spawned less frequently), so we were able to detect signals there. Then we found genetic changes at sequence and expression level. In the talk I explained what the genes whose expression has changed actually do: relate to growth and body size and behaviour," explained Uusi-Heikkilä.

"We often have a high mortality rate in fisheries so we catch a lot of fish. It would be very surprising if this didn't change the genetic pool and cause evolutionary changes."

A road to recovery?​

The team also investigated how the fish would respond when harvesting stopped and to what extent they might recuperate, accounting for six generations of zebrafish.

"This aspect has been studied experimentally a bit, but that was only at the phenotypic level," said Uusi-Heikkilä. "Our raw data points towards phenotypic recovery being slow, and we can see in our case that fish size is not reversing and they are not as large as they used to be."

"More interestingly, what other people haven't done is study this at the genetic level to find out that these genetic changes induced by size-selective harvesting, do not seem, based on our results, to disappear entirely. A little bit erode, but not fully. So in six generations of no harvesting we don't see a full genetic recovery."

"One thing is to notice that these changes can occur quite rapidly. In this case only five generations. It's quite a rapid change but often it takes much longer to reverse."

This rebounding of the genetic expression among the stock is the point Uusi-Heikkilä considers to be of greater significance.

"The populations didn't recover as quickly as changes were induced. So it seems we can cause these differences – we can make the fish small really, really quickly. But then if we think we can just wait for a few generations and they will be large again, we can see that isn't actually the case. It takes much longer for the populations to recover than it did for them to get small."

Well-framed science

In being considered the best presentation at this year's conference, the study was acclaimed by the Awards Committee both for the ambitiousness of its science and the clear way it was laid out and narrated.

"I don't think there's ever any harm in trying to keep things as simple as possible and avoiding genetic jargon that doesn't say that much to all of the people. I think that's one of the key elements and why people found it easy to follow," she concluded.​​

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Silva outside the laboratory, holding a perch. 

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A winning expression of gene expression

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