Birds, descendants of dinosaurs, witnessed the demise of all other dinosaur lineages during the Late Cretaceous mass extinction. However, the ancestors of the vast majority of extant bird species rapidly proliferated and diversified into numerous new groups in less than 10 million years, a remarkable evolutionary feat.
Yet, for over a century, the internal relationships within the genealogy of extant birds remained unresolved, posing a significant challenge to constructing the tree of life.
On April 2nd, the International Avian Genomic Consortium, spearheaded and predominantly led by Chinese scientists, unveiled a significant research milestone in the second phase of the Avian Genomic Project, reconstructing the tree of life for the evolution of extant birds. This groundbreaking study not only proposes a new classification scheme but also clarifies the relationships among various groups of extant birds. The related paper was published in Nature.
The Genomic Puzzle of Avian Evolution Unveiled
Birds, with over ten thousand extant species, constitute a formidable challenge to taxonomy owing to their diverse evolutionary pathways. Classified within the avian subclass, they are broadly categorized into two main groups: the Paleognathae and Neognathae.
Paleognathae encompasses a plethora of flightless birds, while Neognathae further divides into the Galloanserae and Neoaves. The former includes familiar species like chickens, ducks, and geese, whereas the latter, comprising 95% of extant birds, represents the bulk of avian diversity today.
According to Professor Jon Fjeldsa?, a lead author of the study and Chair Professor at the Center for Life Sciences and Evolutionary Research at Zhejiang University, the Neoaves underwent a rapid species radiation in history, giving rise to numerous avian lineages within less than ten million years, essentially shaping the contemporary global diversity of avian species.
"The rapid radiation poses significant challenges in elucidating the evolutionary relationships among various groups within the Neoaves, leading to a chaotic classification of extant birds at the 'order' and 'family' levels, lacking a unified understanding," noted Professor Fjeldsa?.
Rapid radiative evolution is the process where ancestral species rapidly give rise to multiple species groups within a short timeframe. Dr. Josefin Stiller, a co-author of the paper and researcher at the Center for Life Sciences and Evolutionary Research at Zhejiang University, explained that the challenges in determining phylogenetic relationships among groups stem from phenomena such as incomplete lineage sorting of genes and hybridization across species during this process. Thus, identifying analytically effective loci becomes crucial.
In 2020, the International Avian Genomics Consortium published findings in Nature, employing a reference-free whole-genome sequence alignment method to establish homologous sequences across 363 avian genomes, covering 92% of avian orders and families, thereby offering insights into avian 'family'-level systematic relationships.
Revolutionizing the Avian Tree of Life
Over the past century, researchers in avian systematic taxonomy have proposed various perspectives on the phylogenetic relationships among major groups within Neoaves using different data types such as morphological data, mitochondrial data, sequences of a few protein-coding genes, and avian species genomic data, sparking numerous debates.
"Our research rectifies misconceptions from previous studies and brings about significant adjustments to the previously assumed evolutionary relationships," explained Chen Guangji, a co-author of the paper and doctoral student at the University of Chinese Academy of Sciences. This new classification scheme delineates four major evolutionary branches within Neoaves, including not only the existing groups of Mirandornithes, Columbea, and Telluraves but also introduces a novel clade, Eleutherornithes.
Eleutherornithes encompasses both aquatic birds like penguins, divers, albatrosses, as well as terrestrial species like bustards, and birds of prey like owls and swifts, named after the three elemental habitats: water, land, and air.
Previous studies dispersed these bird groups across different evolutionary branches. However, this research demonstrates that they actually originate from a single clade, diverging from a common ancestor.
In addition to clarifying classification relationships, the timing of the rapid radiative evolution of early Neoaves has long been debated. The origin of birds is linked to the dinosaur extinction event about 66 million years ago. However, there have been two distinct views in academia regarding whether the rapid diversification of Neoaves occurred before or after this extinction event.
"The 'mass survival' hypothesis suggests that the rapid radiation of Neoaves occurred before the mass extinction event, implying that Neoaves diversified rapidly, and multiple Neoaves groups survived the global changes caused by the asteroid impact," said Dr. Feng Shaohong. "Our constructed avian phylogenetic time tree supports the 'big bang' hypothesis," Dr. Feng continued, indicating that the rapid diversification of Neoaves occurred after the mass extinction event, benefiting from the ecological niches vacated by the event, allowing for rapid adaptive radiation.
"Our study employs a challenging approach to construct the tree of life for avian species, aiming to clarify relationships and resolve controversies," explained Chen Guangji. Traditional studies in phylogenetic relationship construction often rely on conserved genomic regions such as protein-coding sequences and ultra-conserved elements. However, these regions, under strong selective pressures to maintain protein structure and function, exhibit complex evolutionary patterns.
"We believe that regions with lower selective pressures might be more suitable for study, such as intergenic sequences," added Chen Guangji.
As a result, the research team constructed a large-scale, cross-species, whole-genome comprehensive dataset of intergenic regions to unravel the mystery of avian phylogenetic relationships.
The findings reveal that approximately 89% of 361 avian ancestral evolutionary nodes can be resolved using a small amount of intergenic sequence data. A small portion of ancestral nodes can be reliably resolved by increasing data quantity, while a very small number of complex nodes remain difficult to resolve even with increased data.
Furthermore, in comparing strategies to increase species quantity versus data quantity, the research team found that enhancing effective data quantity is more critical. "In our research, it's evident that intergenic sequences serve as a more ideal choice for reconstructing phylogenetic relationships. Moreover, in large-scale evolutionary studies, ample and effective data prove crucial in resolving complex evolutionary histories at challenging nodes," remarked Chen Guangji during a discussion on research insights.
Related paper: Link to the paper
