Complexity of avian evolution revealed by family-level genomes

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Complexity of avian evolution revealed by family-level genomes

Abstract
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method, and the choice of genomic regions 1–3. Here, we address these issues by analyzing genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Paleogene (K–Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K–Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

https://www.nature.com/articles/s41586-024-07323-1

@John_Harshman
The publication date is 4/1, but I assume this is serious. :wink:

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You were thinking maybe that there’s some subtle bird-phylogenetics joke that you just aren’t getting? No this is straight. There’s a companion paper that I would cite here if I wasn’t far from my computer.

[Later] Ah, here it is:

https://www.pnas.org/doi/10.1073/pnas.2319506121

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I’ll look for it.

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This reminds me of something I saw recently:

The hoatzin was originally described in 1776 by German zoologist Statius Müller. Much debate has occurred about the hoatzin’s relationships with other birds. Because of its distinctness, it has been given its own family, the Opisthocomidae, and its own suborder, the Opisthocomi. At various times, it has been allied with such taxa as the tinamous, the Galliformes (gamebirds), the rails, the bustards, seriemas, sandgrouse, doves, turacos and other Cuculiformes, and mousebirds.[5] A whole genome sequencing study published in 2014 places the hoatzin as the sister taxon of a clade composed of Gruiformes (cranes) and Charadriiformes (plovers).[11] Another genomic study in 2024 instead places it as the sister group to the Phaethoquornithes (containing numerous aquatic bird orders). The combined group was found to be sister to the Mirandornithes (flamingos and grebes).[12]

In 2015, genetic research[13] indicated that the hoatzin is the last surviving member of a bird line that branched off in its own direction 64 million years ago, shortly after the extinction event that killed the nonavian dinosaurs.[14] Another genetic study from 2024 instead suggested a Late Cretaceous origin (around 70 million years ago), but found that this early divergence is shared with a majority of extant bird orders, making it no more primitive than them.[12] [Wikipedia]

[Hat-top Jerry Coyne]

It seems that they can’t make up their mind where to place that darn Hoatzin.

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True enough. It’s been the bane of bird phylogeny since forever, and the current paper makes slight progress at best.

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