A frozen piece of genome rewrites our understanding of the bird family tree
[8 Aprile 2024]
65 million years ago, a huge meteorite spelled the end for most, but not all, dinosaurs, as birds, technically dinosaurs with wings, thrived next.
Scientists have spent centuries pedigreeing around 10,000 bird species to understand how the last surviving dinosaurs conquered the skies, and cheap DNA sequencing should have made it easier, as it has for countless other species. But apparently the birds fooled them.
In fact, two new studies – “A region of suppressed recombination misleads neoavian phylogenomics” Published on Proceedings of the National Academy of Sciences (PNAS) by a team of researchers led by Siavash Mirarab who teaches computer engineering at the University of California San Diego (UCSD), and “Complexity of avian evolution revealed by family-level genomes“, Published on Nature by a team of researchers led by Josefin Stiller of Københavns Universitet – reveal that another event 65 million years ago misled scientific research from the true history of birds and discovered that «A section of a chromosome remained frozen in time for millions of years and refused to mix with nearby DNA as it should have.” This section, just 2% of the bird genome, convinced scientists that most birds could be grouped into two main categories, with flamingos and doves as evolutionary cousins. The most accurate family tree, which takes into account the misleading section of the genome, identifies 4 main groups and identifies flamingos and doves as most distantly related.
Both studies are part of the B10K avian genomics project led by Guojie Zhang of Zhejiang University, Erich Jarvis of Rockefeller University and Tom Gilbert of Københavns Universitet
Biologist Edward Braun of the University of Florida, senior author of the study published in PNAS, explains that «My laboratory has been working on this problem of bird evolution for longer than I would like to think. We had no idea that a large portion of the genome was behaving in an unusual way. We kind of stumbled upon it.”
Braun oversaw the international team of researchers led by Mirarab, who published evidence that this “sticky” piece of DNA confused the true story of bird evolution.
Mirarab and Braun also contributed to the study published in Nature which outlines the updated bird family tree and confirms that Neoaves, a group comprising the vast majority of bird species, underwent a rapid radiation at the Cretaceous to Aleogene (K-Pg) transition. The researchers write that «Evaluation of the impacts of different genomic partitions showed high heterogeneity in the genome. We discovered strong increases in effective population sizes, replacement rates, and relative brain sizes following the K-Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate provides new insights into the rapid radiation of modern birds and provides a taxon-rich backbone for future comparative studies.”
But by December 2014, Braun and his collaborators had published on Science the study “Whole-genome analyzes resolve early branches in the tree of life of modern birds” which drew a family tree for the Neoaves.. Based on the genomes of 48 species, they divided the Neoaves into two broad categories: doves and flamingos in one group , everything else in the other. Repeating a similar analysis this year using 363 species, a different family tree emerged that divided doves and flamingos into two distinct groups.
Holding two mutually exclusive family trees, scientists tried to figure out which tree was correct and Braun. “When we looked at the individual genes and which tree they supported, it suddenly turned out that all the genes that support the older tree are all in the same place,” he says. That’s what started it all.”
Examining this, Braun’s team noticed that it was not as mixed as it should have been after millions of years of sexual reproduction. The researchers further explain: «Like humans, birds combine the genes of a father and a mother in the next generation. But both birds and humans first mix the genes they inherited from their parents when creating sperm and eggs. This process is called recombination and maximizes the genetic diversity of a species by ensuring that no two siblings are alike.”
Braun’s team found evidence that a section of a bird’s chromosome had suppressed this recombination process for a few million years, around the time dinosaurs disappeared. It is unclear whether the extinction event and the genomic anomalies are related.” The result is that «In this frozen piece of DNA, flamingos and doves looked similar to each other. But by taking the entire genome into consideration, it became clear that the two groups are more distantly related.”
Braun adds: “What is surprising is that this period of suppressed recombination could mislead the analysis. And because it might mislead the analysis, it would actually be detectable more than 60 million years into the future. This is the beautiful part. A similar mystery could also hide in the genomes of other organisms. We discovered this misleading region in birds because we have invested a lot of energy in sequencing bird genomes. I think there are cases like this out there for other species that are simply not known at this time.”
