Whole-genome analyses resolve early branches in the tree of life of modern birds

By Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer, Bo Li, P. Houde, Cai Li, Simon Y. W. Ho, B. Faircloth, B. Nabholz, Jason T. Howard and 95 more. Science, 2014

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To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/ee5cf1dafaa6d54f03bac9543225dda2a238b114

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Citations in the corpus

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees (2018, methodology): “Shown are reference trees from the original paper [5] using the coalescent-based binning (a) and”
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Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets (2017, methodology): “, JarvD5a, 48 taxa, and 14,448 genes [Jarvis et al. 2014]), or both (e.”
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IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, neutral): “…protein alignments and introduces a general matrix Q.pfam and a series of new clade-specific matrices—Q.bird, Q.insect, Q.mammal, Q.plant, Q.yeast—derived from large empirical datasets (Jarvis et al. 2014; Misof et al. 2014; Ran et al. 2018; Shen et al. 2018; Wu et al. 2018; El-Gebali et al. 2019).”
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