Defeating the Enemy Within: How Evolution Helps Clone Fish With Its Genetic Burden

Clonal vertebrates do not reproduce sexually. According to scientific theories, they are actually inferior to other species. The Amazon molly - a particularly successful natural clone - proves the opposite. A research team led by Dr. Yuan Lu and Dr. Manfred Schartl, co-PIs of the Xiphophorus Genetic Stock Center at Texas State University, has shown that this small fish has found a way over a hundred thousand years to deal with the challenges of its origin and reproduction.

Clonal Hybrids have hard times to survive:

Clonal vertebrates originated mostly from the accidental rare mating of two closely related species, so they are hybrids. One of these species is the Amazon molly, named after the female warrior tribe of the Amazons from Greek mythology. The Amazon molly is likely to be traced back to a single animal, the “Prima Eva”, which arose from the mating of a female Atlantic molly with a male Sailfin molly. Amazon molly have existed for more than a hundred thousand years, although according to scientific theories they should have been extinct.

The problem with clonal hybrids is that within pure clones, genetic defects would have to accumulate over the generations until at some point there are no longer any healthy individuals. In addition, because of the lack of a new addition to their genetic make-up, these species are usually unable to adapt to changing environmental conditions as quickly as their competitors, who reproduce in a sexual way. In the course of evolution, in which the principle of "survival of the fittest" applies, they should therefore lose out within a few generations. Another “genomic” problem is the coexistence of two considerably divergent genomes contributed by the two different species from which the parents of the Prima Eva were derived. Such a situation, where dissimilar genomes have to work in concert in the same nucleus creates what is often called a ”genomic shock”. 

Now this study shows that the Amazon mollys have found ways in the course of their hundred-thousand-year evolution to deal with the "burden" of their hybrid origins and even to develop adaptations to the living space. “In another study we found few signs of genetic degeneration in the genome of the Amazon molly, but rather unique genetic variability and clear evidence of ongoing evolution. Now we have also been able to show that these fish have developed mechanisms to successfully regulate both genomes, ”says Professor Manfred Schartl from the Xiphophorus Genetic Stock Center at Texas State University and University of Würzburg.

Exceptional phenomenon of the Amazon molly:

The team examined which genes the animals read from their DNA, that is, which genes are "used". The researchers were able to show that in the Amazon molly both genomes of their ancestors are not read with the same frequency, but that either one or the other genome is used in many genome areas. This regulation prevents the two genomes from interfering with one another.

They also compared the use of genes from two different clone lines. Explanation: Different clone lines arise through natural mutations. They showed that all individuals in a clone line use roughly the same genes - have the same gene expression patterns. These gene expression patterns differed in comparison with the individuals of the other clone line. Not only do the clone lines differ slightly genetically, these differences are also of a functional nature and not accidental. This constancy of the expression pattern within a line is possibly the mechanism that clones have hitherto considered to be lacking for being able to adapt to their respective habitats.

The two genomes that are actually competing may even help with successful adaptation - the Amazon molly have twice as much genetic information available and the long evolution of this species has led to them being able to adaptively control it.

The researchers now want to investigate how the differences in gene expression between the clone lines affect their behavior and other aspects of their lives.

Original publication:
Yuan Lu, David Bierbach, Jenny Ormanns, Wesley C. Warren, Ronald B. Walter, Manfred Schartl. 2021. Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly. Genome Research 31: 1-8

With press release material from Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB) at Humboldt Universität zu Berlin, see: