Fishing for answers in the brown trout genome

From starfish that regenerate their limbs, to Ebola-resistant bats and fungi that could produce biofuels – there is a whole host of phenomena in the natural world that researchers are seeking to understand. And that’s just in the species we know about.

New species, and even entirely new branches of the tree of life, are being discovered all the time^[1]. Some species are found as previously unexplored habitats are surveyed, be that a monkey^[2] on a mountain top, or microscopic fungi in a pond in Exeter^[3]. Others are found as genetic analysis reveals that some species, like giraffes, which have previously been thought of as one, are in fact several separate species^[4]. Our understanding of what a species is, is changing.

Genetic analysis is also a crucial part of understanding how organisms function. The secrets to their unique abilities could be hidden in their DNA.

Researchers worldwide have committed to the Earth BioGenome project’s aim to sequence the genomes - the complete sets of genetic instructions - of all animals, plants, fungi and protists on Earth: some 1.5 million species. To date, the genomes of less than 0.2 per cent of known complex life, or eukaryotes, have been sequenced. The work will undoubtedly uncover new species along the way, as well as aid conservation efforts.

One of the latest species to have its genome sequence determined is the brown trout^[5].

Different forms of brown trout.
Image credits: Eric Engbretson for U.S. Fish and Wildlife Service, David Miller and Jon Beer.

Adaptability

The brown trout, Salmo trutta, is a highly adaptable species, with many forms and behaviours^[6]. Some live in freshwater rivers, ranging over only 200 meters or so in their entire lives. Others are born in freshwater, but swim out to sea and then return to their place of birth to spawn, anywhere from months to several years later^[7]. They’re able to thrive in acidic Scottish Lochs^[8] as well as rivers with high metal contents in Cornwall, and clean waters across the Northern hemisphere.

A fully grown fish can be anywhere from 100 grams to over 57 kilograms depending on the type and location. Researchers are fascinated by the species’ adaptable physiology and genetic diversity. Some suggest that there are, in fact, up to 50 different species^[9].

Trout, like other bony fish, have a second copy of their entire genome. This ‘genome duplication’ occurred in their evolutionary past. A sudden doubling of a complete genome is a rare event, but one that has shaped the evolution of vertebrates^[10]. It results in a ‘spare’ copy of the genome, free to change its functions and specialise in a new way.

The newly released brown trout genome sequence will support research into fish evolution, as well as research into how species adapt and survive in a changing environment.

Managing trout

Brown trout are native to Europe and western Asia with a small number of populations in North Africa. They also have been successfully introduced to countries across the globe. While they are not currently endangered many distinct lineages with unique genetic variations are threatened, including those from North Africa and western Asia. In Europe, many brown trout habitats are under increasing pressure. Due to climate change, water and oxygen levels in rivers are falling, and many lakes are becoming more acidic.

Setting ‘biological reference points’^[11] is a goal for those who manage UK populations of trout. These points act as benchmarks for a particular location in terms of how many fish should be there to ensure the health of the river or lake, as well as a harvestable surplus.

“Trout are an economically important species and we’re only just beginning to understand how diverse these fish are. Understanding the genetics of the trout will help us set the biological reference points we need. We know that trout from one location have adapted to that specific environment, and this knowledge should inform how we manage rivers and lakes and their trout populations to preserve this remarkable diversity ”

Mark Ives, Fisheries and Aquaculture Scientist at the Centre for Environment, Fisheries and Aquaculture Science

Custodians of the planet

Humans are destroying many of the species we share the Earth with. We are warming the planet and devastating their habitats. The most recent Living Planet Index report found a 58 per cent decline in vertebrate populations during the 42-year period from 1970 to 2012^[12]. By the year 2050, up to 50 per cent of existing species may become extinct, mainly due to natural resource-intensive industries^[13].

We have a duty to protect and conserve biodiversity - understanding the biodiversity on Earth, both within and between species, is a major goal for the Earth BioGenome project. The project will enable researchers and conservationists to better understand species and the ecosystems they live in.

It may be that the brown trout can gives clues about adapting to a changing environment, enhancing efforts to preserve not just trout but other species and their habitats too.