Last December 12, the journal Science included a paper by Erich Jarvis et al. (reference and free download below) that undertook an ambitious revision of the family tree of birds. Although I read it when it came out, I didn’t post about it as I simply didn’t have the time (it takes about 4 hours to read and prepare one of these scientific posts). But I was reminded that I was remiss by a short piece by Sarah Lewin appearing online in March the Scientific American site, “The bird family tree gets a makeover“. The advantage of Lewin’s piece is that it compares both the old and new family trees (“phylogenies”) of birds to show how drastically our view of their evolution has changed from the Jarvis et al. paper. And there’s also a nightjar in both—can you spot it?
I’m only going to show the results, which are based on DNA sequencing of 48 birds spread across all avian orders. Three types of DNA were used: protein coding genes, introns (which are spacer segments separating protein-coding regions of DNA), and UCEs, as described below:
. . . we identified a high-quality orthologous gene set across avian species, consisting of exons from 8251 syntenic protein-coding genes (~40% of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~1000 bp of flanking sequences. This total evidence nucleotide data set comprised ~41.8 million bp (table S3 and SM4), representing ~3.5% of an average avian genome.
The tree that resulted rested largely on noncoding intronic sequences, as one expects, since noncoding DNA is expected to be largely free of selection, and thus its evolution simply reflects the passage of time (evolution by “genetic drift”). This noncoding DNA is precisely the kind of DNA you want when you’re constructing a phylogeny. After all, a family tree simply describes which species’ ancestors branched off at different times, which and that time-branching is the relatedness of moden species. Anything affected by natural selection, whose action is usually not as clocklike, is likely to make the phylogeny noisier. At any rate, here is the new tree presented by Lewin, followed by her conclusions:
The new tree confirms many past observations, such as the common ancestor of the core landbirds. It also resolves some controversial links. Who might have guessed, for instance, that pigeons and flamingos are close cousins?
In addition to 48 bird genomes, the researchers sequenced three crocodilian genomes to pinpoint early descendent relationships.
The separation of penguins, pelicans and ibis from flamingos and grebes (and pigeons) implies that the waterbird trait evolved independently multiple times.
Because of how quickly both land birds and waterbirds evolved, the data suggests that the original ancestors might have been birds that lived along the coastline.
Chickens share the most DNA with the first bird ancestor, closely followed by hoatzin and emu.
You can see how drastically things were revised. What strikes me is first of all, that vocal learning, the ability to imitate and learn new sounds, evolved three times independently: in songbirds like starlings, in parrots (of course), but also in hummingbirds! I was completely unaware that hummingbirds had any imitative capacities.
Other things I find intriguing are that parrots are much more closely related to songbirds than previously thought; that pigeons and doves are now more closely related to flamingos than to other songbirds; that hummingbirds are a sister group to the swifts; that falcons are more closely related to parrots than to either eagles or vultures; and that owls are more closely related to trogons, woodpeckers and trogons than to falcons.
We have many bird experts as readers, so if I’ve made any errors in my elementary explanation, or if there are any other important or suprising findings I’ve failed to highlight, please add them to the comments.
E. D. Jarvis et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331.