Untold story of bird evolution revealed through genetics 

The cataclysmic impact of a giant meteor around 65 million years ago brought an end to the reign of the majority of dinosaur species, leaving behind a void in which birds, the direct descendants of dinosaurs, emerged as thriving survivors. 

This event marks a critical junction in the evolution of birds, which have since exploded into a diverse group of approximately 10,000 species today. 

Comprehensive family tree of birds

Scientists have long struggled to piece together a comprehensive family tree of birds to understand their evolutionary journey across millennia. 

The advent of affordable DNA sequencing technologies promised a resolution to this complex puzzle, simplifying the classification process that has bewildered researchers for centuries, much like it has facilitated the understanding of lineage and relationships across a multitude of other species.

Peculiar DNA fragment in birds

However, the avian world was not without its enigmas. Recent scientific endeavors have found that an event concurrent with the dinosaurs’ demise 65 million years ago had obscured the true lineage of birds. 

This discovery emerged from a pair of groundbreaking research papers released on April 1, which identified a segment of one chromosome that remained in stasis, resisting the natural blending with adjacent DNA regions over the course of millions of years.

This peculiar fragment, representing a mere two percent of the entire bird genome, previously led scientists to believe that the avian family tree could be broadly divided into two major groups, with species such as flamingos and doves considered closely related evolutionary kin. 

Four primary avian groups

The discovery of a more precise family tree, which takes into account the deceptive nature of this genome segment, now proposes four primary avian groups and places flamingos and doves in more distant branches of the evolutionary lineage.

“My lab has been chipping away at this problem of bird evolution for longer than I want to think about,” said senior author Edward Braun, a professor of biology at the University of Florida. “We had no idea there would be a big chunk of the genome that behaved unusually. We kind of stumbled onto it.” 

Conflicting interpretations of the family tree 

Decades ago, Braun and his team embarked on a journey to construct a family tree for the Neoaves, which encompasses the majority of existing bird species. 

Initial analyses based on the genomes of 48 species led to the classification of the Neoaves into two overarching categories, segregating doves and flamingos into one group, with all other species in the opposing group. 

A subsequent analysis involving 363 species, however, produced a divergent family tree that separated doves and flamingos into distinct categories.

Critical new insights into bird evolution

Confronted with two conflicting interpretations of the avian family tree, the researchers delved deeper into the genetic data in search of clues that could clarify which version was correct. 

“When we looked at the individual genes and what tree they supported, all of a sudden it popped out that all the genes that support the older tree, they’re all in one spot. That’s what started the whole thing,” Braun explained.

Suppression of genetic mixing

Further investigations revealed that a specific section of the bird chromosome had not undergone the expected genetic mixing through the process of recombination – a fundamental mechanism in sexual reproduction that ensures genetic diversity within a species. 

This suppression of recombination in a critical genome segment coinciding with the period of dinosaur extinction had caused flamingos and doves to appear more closely related than they truly are when considering the entirety of the genome.

Similar mysteries may exist in other genomes

The discovery of this anomalous genomic region, capable of misleading evolutionary analysis yet detectable more than 60 million years later, is a proof of the complexity of bird evolution and the challenges inherent in unraveling the true history of these avian descendants of dinosaurs. 

Braun highlighted the potential for similar mysteries to exist within the genomes of other organisms, as yet undiscovered due to the lack of extensive genetic sequencing efforts.

“We discovered this misleading region in birds because we put a lot of energy into sequencing birds’ genomes. I think there are cases like this out there for other species that are just not known right now,” Braun concluded.

The study is published in the journal Proceedings of the National Academy of Science.

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