Sometimes called “living fossils,” lungfish are air-breathing lobe-finned fish — believed to resemble most closely the most ancient common ancestors of all vertebrates. Lungfish are bony fish with a well-developed internal skeleton; their lobed fins even have a bone structure similar to that of tetrapod limbs. Whereas some modern lungfish have reduced or lost certain bones and have a cartilaginous braincase, their fins [which contain a single bone (femur or humerus) — connecting them to the body] are a key feature that distinguishes them from most other bony and cartilagenous fishes.
Since 2018, Axel Meyer and Manfred Schartl [evolutionary biologists at the Julius Maximilians University of Würzburg, and their colleagues] have worked to decipher the genomes of lungfish from three continents to better understand vertebrate evolution. They first sequenced that of the Australian lungfish, whose fin bones resemble those in our limbs and those of other land animals. Then they moved on to the African lungfish, whose limb bones are much reduced. Now, they’ve tackled the South American lungfish, which also has reduced fins — and a genome twice the size of its Australian and African cousins.
Included in that massive genome are the organism’s genes (i.e., the instructions for its proteins written in four different chemical “letters” called nucleotides or bases), as well as codes for helpful pieces of RNA. Although the South American lungfish (Lepidosiren paradoxa) has a genome that is ~30 times larger than the human genome, with about 91 billion DNA bases compared to the human genome’s 3 billion, the number of genes (~20,000) is roughly the same in the two species. The vast majority of L. paradoxa’s genome is composed of something else: repetitive stretches called transposable elements that can make copies of themselves and insert those copies elsewhere, back into DNA. [Barbara McClintock discovered “jumping genes” (also known as transposons), which are mobile genetic elements that can change position on a chromosome. She observed this phenomenon while studying maize (corn) and found that these mobile elements could affect expression of other genes, leading to variations in traits, e.g., kernel color. Her groundbreaking work, which contradicted the prevailing view (for several decades) that genes were fixed in place, earned her the Nobel Prize in Physiology or Medicine in 1983.]
The researchers found that ~90% of L. paradoxa’s genome consists of these transposons, compared with ~40% of the human genome. How did the lungfish’s genome become so cluttered with repetitive DNA? Comparing it with other vertebrate genomes revealed its growth has gone unchecked because the South American lungfish has lost key genes whose RNA and protein products put the brakes on transposable elements. All but one of this lungfish’s 19 chromosomes — is the size of the entire human genome — resulting in the problem that it takes a lot of energy to copy that DNA. And, also, the nucleus and cell that encase it must be larger.
A bigger genome can sometimes help an organism adapt to changing conditions. When transposable elements land in or near a gene, they can alter the activity of that gene — which may be beneficial under the right conditions. These mysterious pieces of DNA can even become sources for entirely new genes. However, it can also become a sword of Damocles: i.e., if it is not possible to regulate this entirely new gene that might ensure the viability of the organism. Therefore, it remains unclear why the fish did not evolve new ways to control the spread of these jumping genes.
L. paradoxa’s genome is not the biggest of all living things, however. The New Caledonian fork fern (Tmesipteris oblanceolate), has the largest genome so far, with its 160 billion DNA base pairs (bp). And other plants, e.g., a Japanese shrub named Paris japonica, also has a genome larger than that of the lungfishes.
One GEITPer asked that this article be highlighted and analyzed on the GEITP email blog. To start with, the authors note that the South American lungfish has lost “key genes whose RNA and protein products regulate the number of transposable elements permissible in a genome.” Yet, they fail to speculate that “key genes” they are talking about (or if we even know that such “key genes” exist — in lungfish or other organisms).
Secondly, what might the timeline be, evolutionarily — when lungfish first appeared on Earth? Because specific species of lungfish are found on three continents (Australia, Africa and South America), we can conclude that lungfishes must have existed from more than 180 million years ago, because that is when the breakup of the supercontinent Gondwana occurred — resulting in the continents that would become Australia, Africa, South America, and Antarctica — during the early Jurassic Period. 😊
DwN
Science Oct 2025; News item. doi: 10.1126/science.zmo35m2