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A groundbreaking examine using full genome-scale knowledge has revolutionized our understanding of chicken evolution, revealing new insights into the phylogenetic relationships amongst chicken species. By analyzing a complete dataset of 363 chicken species, the analysis has redefined the avian household tree, figuring out 4 main clades inside Neoaves and shedding mild on the complicated evolutionary historical past of birds. Credit: SciTechDaily.com
The most in depth genomic examine to this point has unveiled how the birds unfold everywhere in the world after mass extinction.
Birds signify the only real surviving lineage of dinosaurs within the current day. Roughly 66 million years in the past, on the transition from the Cretaceous to the Paleogene interval (the Ok–Pg boundary), a catastrophic extinction occasion led to the demise of all non-avian dinosaurs, offering a chance for birds to diversify quickly and occupy a variety of ecological niches.
Neoaves, a various group comprising roughly 95% of all chicken species right now, emerged from this radiation. From the towering condors of the Andes to the diminutive hummingbirds flitting by tropical forests, Neoaves embody a surprising range of types and features.
Despite appreciable efforts to reconstruct avian evolutionary historical past and the impacts of the Ok-Pg occasion utilizing morphological knowledge and molecular knowledge, the exact branching order and relationships among the many neoavian lineages remained contentious.
“Previous studies on small datasets from different genomic regions often produced conflicting results with respect to the topology of bird tree,” stated Guojie Zhang, senior creator of the paper, a chair professor on evolutionary biology in Zhejiang University, and one of many initiators of the B10K undertaking. “In this study, for the first time, we employed full genome-scale data to construct the tree for bird species from almost all representative families.”
Advancements in Genomic Data
This full genomic dataset was produced by the B10K consortium in its second section which incorporates 363 chicken species protecting all main chicken lineages.
The new household tree is breaking new floor within the lengthy journey to unravel the mysteries of chicken evolution. According to this up to date chicken household tree, a bunch containing flamingos and grebes (referred to as Mirandornithes) have been among the many first neoavian lineages to evolve.
Relationships for 363 chicken species based mostly on 63,430 intergenic loci. Credit: Josefin Stiller
The new tree is difficult the organization of Neoaves by classifying this large group into 4 main clades: Mirandornithes, Columbaves, Elementaves, and Telluraves. Elementaves is a newly proposed grouping comprising ca. 14% of all species of contemporary birds together with disparate teams such because the enigmatic hoatzin, shorebirds, hummingbirds, and tropicbirds.
Elementaves is known as to replicate the group’s exceptional range in ecological niches, representing the foremost components of Earth, air, and water. This new household tree resolves some long-standing debates over the relationships amongst avian species and lays a stable basis for finding out avian evolution and trait improvement.
The Impact of Comprehensive Genomic Analysis
By using full genome knowledge throughout 363 chicken species, that is the largest-ever dataset used for phylogenetic analyses of birds. The staff constructed a brand new pipeline to extract over 150,000 areas unfold out throughout the genome.
“We characterized phylogenetic relationships across the entire genome and identified patterns associated with the genomic context and sequence characteristics,” stated Josefin Stiller, the main creator of this examine and an Assistant Professor in evolutionary biology on the University of Copenhagen, “We found that various parts of the genome, for example, individual chromosomes or protein-coding genes, often support vastly different trees. This likely explains why studies that only analyzed certain genomic parts were in conflict.”
Putting collectively high-quality and enormous quantities of knowledge was key to producing a strong phylogenetic tree. The staff found that for many branches, a consensus on their relationships could be reached when a ample quantity of knowledge was used. But the phylogenetic positions for some chicken teams like owls and hawks stay puzzling even with a full-genome scale of knowledge.
Divergence occasions for 363 chicken species based mostly on 63,430 intergenic loci. Credit: Josefin Stiller
“More data does not necessarily produce a better solution,” Zhang stated. Siavash Mirarab, co-senior creator of the examine, a professor {of electrical} and laptop engineering on the University of California, San Diego, added that, “The reason for this may be some complex evolutionary history like ancient cross-mating between two lineages, incomplete lineage sorting, long-branch attraction, and biased DNA sequence content, all of which can interfere with the reconstruction of phylogenetic trees.”
The examine studies new insights on which of those elements affect which branches of the tree, offering a extra complete and real image of the origin of those avian teams. The examine additionally proposes a extra correct time scale for the diversification of contemporary birds, suggesting {that a} speedy radiation occurred at or close to the mass extinction on the Cretaceous–Paleogene (Ok–Pg) boundary and to a lesser diploma shortly after the Paleogene–Neogene boundary.
The researchers discovered that these radiations coincided with exceptional genetic and morphological modifications amongst birds, together with larger mutation charges, smaller physique sizes, and bigger brains, and bigger efficient inhabitants sizes. “This illustrates the power of comparative genomics: by comparing genomes of living species, we can uncover traces of events that happened 66 million years ago,” Stiller stated.
“Our work has changed many traditional views on the evolutionary history of birds. This new family tree will serve as a solid backbone for mapping the evolutionary history of all bird species with important implications for ornithological research and biodiversity studies,” Zhang concluded.
Reference: “Complexity of avian evolution revealed by family-level genomes” by Josefin Stiller, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A. Duchêne, Qi Fang, Yuan Deng, Alexey Kozlov, Alexandros Stamatakis, Santiago Claramunt, Jacqueline M. T. Nguyen, Simon Y. W. Ho, Brant C. Faircloth, Julia Haag, Peter Houde, Joel Cracraft, Metin Balaban, Uyen Mai, Guangji Chen, Rongsheng Gao, Chengran Zhou, Yulong Xie, Zijian Huang, Zhen Cao, Zhi Yan, Huw A. Ogilvie, Luay Nakhleh, Bent Lindow, Benoit Morel, Jon Fjeldså, Peter A. Hosner, Rute R. da Fonseca, Bent Petersen, Joseph A. Tobias, Tamás Székely, Jonathan David Kennedy, Andrew Hart Reeve, Andras Liker, Martin Stervander, Agostinho Antunes, Dieter Thomas Tietze, Mads Bertelsen, Fumin Lei, Carsten Rahbek, Gary R. Graves, Mikkel H. Schierup, Tandy Warnow, Edward L. Braun, M. Thomas P. Gilbert, Erich D. Jarvis, Siavash Mirarab and Guojie Zhang, 1 April 2024, Nature.
DOI: 10.1038/s41586-024-07323-1
