The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome‐scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avia...

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Bibliographic Details
Published inZoologica scripta Vol. 45; no. S1; pp. 50 - 62
Main Author Suh, Alexander
Format Journal Article
LanguageEnglish
Published Oslo Blackwell Publishing Ltd 01.10.2016
Wiley Subscription Services, Inc
Subjects
Bifurcations
Birds
Conflicts
Cretaceous
Forests
Genomes
Genomics
Hypotheses
Mass extinctions
Neoaves
Paleogene
Phylogenetics
Phylogeny
Reproducibility
Speciation
Species extinction
Topology
Trees
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Summary:Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome‐scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avian Tree of Life are now firmly established as reproducible phylogenetic hypotheses. This is to the exception of the deepest relationships among Neoaves. Using phylogenetic networks and simulations, I argue that the very onset of the super‐rapid neoavian radiation is irresolvable because of eight near‐simultaneous speciation events. Such a hard polytomy of nine taxa translates into 2 027 025 possible rooted bifurcating trees. Accordingly, recent genome‐scale phylogenies show extremely complex conflicts in this (and only this) part of the avian Tree of Life. I predict that the upcoming years of avian phylogenomics will witness many more, highly conflicting tree topologies regarding the early neoavian polytomy. I further caution against bootstrapping in the era of genomics and suggest to instead use reproducibility (e.g. independent methods or data types) as support for phylogenetic hypotheses. The early neoavian polytomy coincides with the Cretaceous–Paleogene (K‐Pg) mass extinction and is, to my knowledge, the first empirical example of a hard polytomy.
Bibliography:istex:622DA4B6CA899505909D07D469C313D14628267B
ArticleID:ZSC12213
Fig. S1. Topological discordance of the eight first neoavian branching events in the main trees of (A) Jarvis et al. () and (B) Prum et al. ().Fig. S2. (A) Majority-rule consensus tree based on Fig.  and (B) simulated nine-taxon polytomy based on a sample of 100% of the 512 possible retroposon presence/absence patterns. Colour coding of phylogenetic networks corresponds to Fig. .Fig. S3. Consensus networks of (A) 3,679 UCE gene trees and (B) 2,022 binned intron gene trees from Jarvis et al. (2014).
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ISSN:0300-3256
1463-6409
1463-6409
DOI:10.1111/zsc.12213