Institute of Molecular Genetics of the Czech Academy of Sciences
For decades, scientists believed that birds were missing an astonishing number of genes found in virtually all other vertebrates. Had these genes truly disappeared during evolution, or had researchers simply failed to detect them? A research team led by Daniel Elleder at the Institute of Molecular Genetics of the Czech Academy of Sciences, in collaboration with Jiří Nehyba, has now shown that the answer is more complex. Some of the “missing” genes had been hidden all along in regions of the avian genome that were difficult to sequence, while others had genuinely been lost during evolution. The researchers also identified a previously unknown form of genetic instability, which they named sequence stuttering.
Today, scientists have decoded the complete genomes of thousands of animal species. Yet bird genomes have long presented an intriguing puzzle. Compared with other vertebrates, they appeared to lack hundreds of genes that evolutionary theory predicted should be present.
For more than a decade, evolutionary biologists debated whether birds had genuinely lost these genes over millions of years or whether the apparent absence simply reflected the limitations of earlier sequencing technologies.
“For a long time, we didn’t know whether we were looking at genuine gene loss or merely a technical limitation. Thanks to newly available genome assemblies and modern sequencing technologies, we were finally able to distinguish between the two,” says Daniel Elleder of the Institute of Molecular Genetics of the Czech Academy of Sciences.
The key to solving the mystery turned out to be the smallest avian chromosomes, known as dot chromosomes. These miniature chromosomes contain exceptionally high proportions of the nucleotides guanine (G) and cytosine (C), making them among the most difficult regions of the bird genome to sequence accurately.
It was here that many of the supposedly missing genes had been hiding. To conventional genome sequencing approaches, these genes were practically invisible. They appeared to be absent even though they had been present all along.
The study also revealed that not all genes had simply remained hidden. Birds have in fact lost approximately one-third of the genes located on dot chromosomes—far more than on any other chromosome type. This process began more than 200 million years ago, well before modern birds evolved, and continued after the major avian lineages had already diverged.
While investigating these chromosomes, the researchers made another unexpected discovery. Within the non-coding regions of genes located on dot chromosomes, they found repeated copying of short DNA segments—a phenomenon they named sequence stuttering.
This newly described form of genetic instability causes short stretches of DNA to be copied repeatedly, somewhat like a speaker involuntarily repeating parts of a sentence. In some cases, fragments of neighbouring coding sequences also become incorporated into these repeated regions.
The extent of this variability proved remarkable. The researchers found substantial length differences in most of the introns located on dot chromosomes. By contrast, such variability was much less common on larger chromosomes, suggesting that sequence stuttering is not merely an ancient evolutionary relic but an ongoing process shaping bird genomes today.
“Imagine a book in which a few sentences change slightly with every new edition. We found something remarkably similar in certain regions of bird DNA. It suggests that these parts of the genome are far more dynamic than we previously thought,” says Daniel Elleder.
It remains unclear whether sequence stuttering directly contributes to gene loss or whether it is another consequence of the unusual properties of dot chromosomes. Either way, the discovery raises new questions about genome stability and how genetic information changes over evolutionary time.
The study demonstrates that the long-standing mystery of the missing avian genes cannot be explained by a single mechanism. Some genes had simply escaped detection by earlier sequencing technologies, while others were genuinely lost during evolution. The discovery of sequence stuttering also provides fresh insights into why certain regions of the genome are considerably more unstable than others.
“Our work shows that even in the era of massive genomic datasets, new technologies can fundamentally reshape our understanding of evolution. Even DNA that appears to have been thoroughly explored can still hold remarkable surprises,” concludes Daniel Elleder.
Hron T, Miklík D, Pačes J, Pajer P, Pečenka V, Hejnar J, Nehyba J, Elleder D: Decoding the Avian Missing Gene Mystery: Dot Chromosomes Unmask Extensive Gene Loss and Novel Genetic Instability. Genome Biol Evol. 2026 18(3):evag038. [pubmed] [doi]