Source of tilapia diversity now a threat to survival

New research led by the Earlham Institute has revealed the impact of ancient and contemporary hybridisation - where an individual reproduces with a closely-related species - on the diversification and genetic resilience of tilapia.

East Africa is a hotspot for tilapia diversity, with some species showing remarkable environmental adaptations, such as tolerance of high salinity, alkaline lakes, and temperature extremes.

However, fish farm escapees and the introduction of non-native species to boost fisheries have led to hybridisation that is presenting a threat to this native biodiversity, as well as local aquaculture.

Global production of tilapia in 2022 was estimated at almost 5.3million tonnes and it has become an important source of protein and nutrients to millions worldwide. Breeding improved strains of tilapia is a cornerstone of providing long-term global food security.

Selective breeding with native populations may be used to generate these regionally optimised aquaculture strains. This can provide genetic material for adaptation to local conditions.

For example, crossing farm strains with salinity-tolerant species could enable aquaculture production in regions where fresh water is scarce by giving farmed fish tolerance of saltier water.

Hybridisation with invasive species, however, could lead to this diversity being ‘watered down’ or lost from native populations before it has even been discovered.

Dr Adam Ciezarek, research author based at the Earlham Institute during the project and now at the Centre of Environment, Fisheries, and Aquaculture Science (Cefas), said: “Because hybridisation has become a recent problem, we wanted to look back in evolutionary time to see how common it was, as well as the impact on the genome. Nobody had studied this with genomic data in tilapia before.”

To understand the historic role of hybridisation, a team of collaborators from the UK and East Africa studied the genomes of 575 individuals from 23 Oreochromis species, the genus to which tilapia belong.

The fish came from drainage basins across Tanzania. This network of rivers and pools between water bodies creates occasional and unpredictable opportunities for the fish to cross-breed.

They initially chose a subset of these fish, whose genome sequences indicated they weren’t recent hybrids. From these genomes, they produced phylogenetic trees - a way of visually representing how closely related two organisms are in evolutionary terms. These trees revealed signals of genes being transferred between species, a hallmark of hybridisation.

The researchers were able to show that hybridisation had historically been a benefit to tilapia, driving diversification and helping them to adopt different ecological niches. In one case, this led to the emergence of a new species - Oreochromis chungruruensis.

This species only lives in Lake Kiungululu, an isolated crater lake in the south of Tanzania, and appears to have originated from hybridisation between two species found close by in the Lake Malawi basin.

“Hybridisation has been an important historic process for tilapia diversification,” said Dr Wilfried Haerty, study author and group leader at the Earlham Institute. “When combined with the unique geography of the region, it has allowed these fish to rapidly adapt and thrive.”

By then comparing the genomes of recent hybrids with the ‘reference’ native species for each water body, the team revealed the detrimental effect of contemporary cross-breeding.

“Ancient hybridisation was likely to be sporadic and opportunistic,” explained Dr Ciezarek. “Human activity has changed the dynamics of the process and may present a significant threat to some native populations.”

Another challenge is that some fish farmers take their farm stocks from the wild, mistakenly assuming they’re catching native tilapia from water bodies when they may actually be catching hybrids.

This could make it less likely that the farm succeeds as, unless carefully selected, hybrids are less likely to grow and reproduce well.

“There’s an education piece as well as some scientific solutions,” said Dr Haerty. “We need to work with people on the ground so they understand the impact of certain practices, while also empowering them with the technology to identify native fish from hybrids.”

The project was conducted by partners at the Earlham Institute, University of Roehampton, University of Bangor, University of Bristol and University of East Anglia - together with partners on the ground, including the University of Nairobi, South Eastern Kenya University, Buginyanya Zonal Agricultural Research and Development Institute, Tanzania Fisheries Research Institute, and the National Museums of Kenya.

The resequencing of the tilapia genomes was made possible thanks to the Technical Genomics group at the Earlham Institute, particularly through their Low Input, Transposase Enabled (LITE) protocol for custom library construction.

The research is published in the journal Molecular Biology and Evolution and was funded by the Biotechnology and Biological Sciences Research Council, Natural Environments Research Council, BBSRC Global Challenges Research Fund, and Leverhulme Trust Africa Awards.