This post is for the birds

Note: this post was has been corrected to reflect the fact that Flamingoes and Pigeons are not sister species, but members of sister clades.
Darwin’s favorite bird, the pigeon, has a new sister (clade) that includes Flamingoes and Grebes. This somewhat surprising result came from a recent phylogenomic analysis of 48 bird species published last week in Science. This analysis and its 27 companion papers were the culmination of years of work conducted by the Avian Phylogenomics Project, which is led by Erich Jarvis, a Professor of Neurobiology at Duke University, Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, and M. Thomas P. Gilbert of Natural History Museum of Denmark.
In this post I take you on a supervised speed date with 12 of the 28 papers:

Erich D. Jarvis, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds, Science (2014).
Whole-genome sequencing of 48 species from all orders of Neoaves provides resolution to the phylogeny of birds. Interestingly, phylogenies generated from exons were often incorrect due to convergence of protein-coding regions (see Fig. 4 in the paper).
Guojie Zhang et al. Comparative genomics reveals insights into avian genome evolution and adaptation, Science (2014) .
Birds have the smallest genomes among amniotes – weighing in at about 0.9 to 1.3 Gb (Fun fact: the largest genome is also from the largest bird – the ostrich.) Many avian genomes show signs of selection at many functionally relevant loci that may be involved in bird-specific phenotypes including, flight, color vision and song learning.
Qi Zhou et al. ‘Complex Evolutionary Trajectories of Sex Chromosomes across Bird Taxa’, Science (2014).
Male mammals have a Y chromosome, while female birds have a W chromosome. In contrast to the mammalian Y-chromosome (which is not dead!), most bird W chromosomes are not completely degenerate (except for the chicken) and are surprisingly variable across species – possibly as the result of sexual selection.
Andreas R. Pfenning et al. ‘Convergent Transcriptional Specializations in the Brains of Humans and Song Learning Birds’, Science (2014).
Humans and songbirds are both vocal learners and, interestingly, they have converged on similar brain pathways that have enable this ability to learn song (and speech). This paper used microarrays to measure gene expression in song control regions of the bird brain, which revealed that convergent evolution of some transcriptional networks in song and speech-associated brain regions.
Osceola Whitney et al. ‘Core and Region Enriched Networks of Behaviorally Regulated Genes and the Singing Genome’, Science (2014).
More birdsong related findings! Singing significantly altered the expression of ~10% (n=2740) of the genes in four major song control regions. This paper also thoroughly described the molecular mechanisms that underly these behaviorally-regulated gene networks, which include variation in transcription factor binding and “primed” regions of open chromatin in enhancers and promoters.
Siavash Mirarab et al. ‘Statistical Binning Enables an Accurate Coalescent-Based Estimation of the Avian Tree’, Science (2014).
This paper describes the “statistical binning” method developed to resolve the avian phylogenetic tree, which has been complicated due to incomplete lineage sorting
Robert W. Meredith et al., ‘Evidence for a Single Loss of Mineralized Teeth in the Common Avian Ancestor’, Science (2014).
Newsflash! Birds don’t have teeth. In fact this study found that nearly all birds share inactivating mutations in genes that are involved in making and maintaining your chompers, suggesting that this toothless trait is deeply rooted in the avian tree.
Check out all of these new genomes!
Michael D. Shapiro et al ‘Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon’, Science, (2013).
What do you get when you breed a bunch of different fancy pigeons? A rock pigeon! This paper generated a rock pigeon reference genome and also identified a strong candidate gene, EphB2, for the head crest that is shared across many fancy pigeon breeds.
Shengbin Li et al. ‘Genomic Signatures of near-Extinction and Rebirth of the Crested Ibis and Other Endangered Bird Species’, Genome Biology (2014).
Many bird species are threatened and one, the crested ibis, was almost extinct in the wild as of 30 years ago. Here, Li et al sequenced and used the crested ibis genome to draw insights into how molecular breeding and conservation can help save and recover populations of endangered and threatened birds.
Richard E Green et al. ‘Three Crocodilian Genomes Reveal Ancestral Patterns of Evolution among Archosaurs’, Science (2014).
Green et al sequenced the genomes of three extant crocodilians – birds close phylogenetic relative – and found that croc genomes evolve really slowly. In combination with the avian genomes, they were able to reconstruct (with 91% accuracy) the partial genome of the common ancestor of birds, dinosaurs, and crocodilians.
Ganeshkumar Ganapathy et al. ‘High-Coverage Sequencing and Annotated Assemblies of the Budgerigar Genome’, GigaScience, (2014).
Here comes the parakeet genome. This new reference genome of a single Australian parakeet, aka the budgerigar, paves the way for research on the genomic mechanisms underlying some of the unique traits of parrots – from dancing to the Backstreet Boys to mimicking the vocalizations of other species.
Cai Li et al. ‘Two Antarctic Penguin Genomes Reveal Insights into Their Evolutionary History and Molecular Changes Related to the Cold Antarctic Environment’, GigaScience (2014).
The sequencing of two penguin genomes revealed that they have undergone a population expansion since the last glaciation and that they have genes and gene families that may have evolved to them keep warm in the Antarctic.
If you want to learn even more about avian genomes you can find links to all of the avian genomic papers here.