A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

  title={A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing},
  author={Richard O. Prum and Jacob S. Berv and Alex Dornburg and Daniel J. Field and Jeffrey P. Townsend and Emily Moriarty Lemmon and Alan R. Lemmon},
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence… 
Evolution: An avian explosion
Targeted genomic sequencing from 198 living bird species provides an unprecedented combination of breadth and depth of data, and allows the most robust resolution so far of the early evolutionary relationships of modern birds.
Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification
The DNA-based phylogeny indicates that rails underwent an initial split into 2 groups ∼34 mya, and that 9 major extant rail lineages have evolved since then, form the basis for a proposed classification of the Rallidae that recognizes 40 genera in 9 tribes.
A Phylogenomic Framework, Evolutionary Timeline, and Genomic Resources for Comparative Studies of Decapod Crustaceans
It is shown that crown decapods diverged in the Late Ordovician and most crown lineages diverging in the Triassic-Jurassic, highlighting a cryptic Paleozoic history, and post-extinction diversification.
DNA Analyses Have Revolutionized Studies on the Taxonomy and Evolution in Birds
  • M. Wink
  • Biology
    Birds - Challenges and Opportunities for Business, Conservation and Research
  • 2021
Whereas Linné aimed to classify all species of the authors' planet by a unique binomial Latin name, later generations of taxonomists and systematicists intended to place the taxa in a natural system according to their phylogeny, still scientists are on the way to find the ultimate “Avian Tree of Life”.
Birds in a bush: Toward an avian phylogenetic network
The usefulness of phylogenetic networks to capture the complexity and subtleties of diversification processes by discussing several recent genomic analyses of birds in general and the well-known radiation of Darwin's finches is illustrated.
Dense sampling of bird diversity increases power of comparative genomics
The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA.
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.


Phylogeny and diversification of the largest avian radiation.
The historical framework suggests multiple waves of passerine dispersal from Australasia into Eurasia, Africa, and the New World, commencing as early as the Eocene, essentially reversing the classical scenario of oscine biogeography.
A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.
The first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, is performed to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution, finding no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unitOf time, as recently suggested.
Whole-genome analyses resolve early branches in the tree of life of modern birds
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
A new classification for the order Coliiformes is proposed including two new families, Chascacocoliidae and Selmeidae, and it is suggested that the Lower Eocene Eocolius is the most basal member of clade Coliidae, while the Lower–Middle Eocene Sandcoleidae form a basal clade with respect to all other known coliiforms.
A Phylogenomic Study of Birds Reveals Their Evolutionary History
This study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods.
Molecular Phylogenetics and the Diversification of Hummingbirds
Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon
DNA sequences from the large nuclear RAG-1 exon are used to investigate the phylogenetic relationships of the avian family Accipitridae and found strong support for a monophyletic clade comprising the secretarybird Sagittarius serpentarius, the osprey Pandion haliaetus, and the traditional accipitrids.
Phylogenomics resolves the timing and pattern of insect evolution
The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
The global diversity of birds in space and time
It is found that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present, with a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers.
The phylogeny of the living and fossil Sphenisciformes (penguins)
The results do not support an expansion of the Spheniscidae from a cooling Continental Antarctica, but instead suggest those species that currently breed in that area are the descendants of colonizers from the Subantarctic.