Stunning report of the complete mapping of the genomes of 48 birds, representing the entire family tree

[jimmy]

This is a stunning Washington Post report on the 8 papers released in Science and 20 companion articles in other journals, that mapped the complete genomes of 48 birds, each of which represents separate lines.  Attached is a copy of  that family tree.

 Among the findings: crocodiles are more closely related to birds than other reptiles, enabling the reconstruction of the common ancestor of birds, dinosaurs and crocodiles; the same genes that permit birdsong is responsible for human speech; 115 million years ago a common ancestor of birds lost the ability to coat teeth with enamel, marking the shift from teeth to beaks; chickens are more closely related to the ostrich than the pigeon; instead of the picture of broad speciation of birds BEFORE the extinction of the species diversity boom of birds happened after, and few birds survived that extinction. 

This is a sweeping vision of Time across the epochs. This is just a tease: look at the chart of the family tree of the birds and read the article, or the journals for more (see at the bottom).

from the Washington Post:

 

Genome project maps the bird family tree, unlocking their dinosaur pasts

 

The Washington Post by Rachel Feltman December 12, 2014 p A. 3.

It’s a fine-feathered week for science.  On Thursday, the journal SCIENCE published eight papers on birds, with an additional 20 appearing in other journals over the next few days – and for good reason.

The flagship study of the bunch announces that 48 birds (at least one from every major bird lineage) have had their entire genetic code uncovered. Until now, scientists only had a handful of common birds to work with. This massive increase in data has allowed researchers to uncover new information about the origin of birds, the genes and brain mechanisms that drive their behavior, and their relationships to each other — findings described in the additional papers.

In other words, scientists essentially completed the bird family tree.

That’s a tricky tree to plant. Birds, the most species-rich class of four-limbed vertebrates, are the surviving descendants of dinosaurs. But understanding why birds survived while other dinos didn’t (and how they grew so diverse) has been a mystery. Modern birds split into different species millions of years ago, so it’s difficult for scientists to pinpoint when and how they diverged from common ancestors.

The collection of new studies is the first solid step in answering those questions. In one paper, for example, scientists used modern genomes to reconstruct the genome of an ancient organism — the last common ancestor of crocodiles, birds and dinosaurs.

Crocodiles, which have evolved slowly, are more closely related to dinosaurs and birds than to other living reptiles. Once researchers had the new genome information from birds, they were able to piece together what a common ancestor would have looked like — or what its DNA would have looked like, anyway. This will help scientists study past and present animals from that branch of the tree of life.

And the new genetic information helps tell the story of how birds survived the mass extinction of the dinosaurs: Some have suggested that birds separated into many different species about 10 million years before the mass extinction that killed dinosaurs, but these studies suggest that the species boom occurred after. It’s likely that only a small number of birds survived the extinction, the researchers report. With so many evolutionary niches left empty by newly extinct animals, birds were able to evolve into a wild collection of different species.

The international genome-mapping effort took the work of 200 people from 80 labs and several months of data-crunching with a supercomputer. The 48 sequences were completed between 2010 and 2011, but it took three years to create an accurate family tree.

 “It is very satisfying to finally have answers to questions that have not been crystal-clear from the fossil record,” said Mark Springer, a professor of biology at the University of California at Riverside and lead author of one of Thursday’s related papers. “Our results highlight the power of DNA from the crypt to unravel the evolutionary history of vertebrates. Together, genomic fossils and fossils from rocks provide a powerful combination for reconstructing the past.”

Springer and his collaborators used the data to answer a long-standing question about bird teeth (or the lack thereof). Scientists knew that birds had descended from toothy dinosaurs, but the fossil record has been too spotty to pinpoint the day of tooth decay.

Now, he and his colleagues report, they’ve traced the gene mutations that prevent the formation of tooth enamel back 116 million years. That’s when birds started switching teeth for beaks.

Duke University neuroscientist Erich Jarvis, who co-led the sequencing effort with Guojie Zhang of the Beijing Genomics Institute and M. Thomas P. Gilbert of the Natural History Museum of Denmark, used the data to study birds that can learn to sing certain songs. This mechanism is thought to be a close mirror of human speech.

Sure enough, the genes that enable birds to sing seem to be the same ones that allow humans to speak. Birds can be used in the lab to help scientists better understand the mechanics of human speech and how speech evolved.

Related:

How birds lost their teeth

Unlocking bird’s dinosaur past

Connecting birdsongs and human speech

Study: American birds struggle to survive

 

from the Science journal summaries: 

Science 12 December 2014:
Vol. 346 no. 6215 pp. 1308-1309
DOI: 10.1126/science.346.6215.1308

Introduction to Special Issue A flock of genomes

1.     Guojie Zhang,

2.     Erich D. Jarvis,

3.     M. Thomas P. Gilbert

Characterization of genomic biodiversity through comprehensive species sampling has the potential to change our understanding of evolution. To study evolution across a major vertebrate class, dissect the genomics of complex traits, and resolve a centuries-old debate on the avian species tree, we formed a consortium focused on the sequencing and analyses of at least one genome per avian order. The resulting data set of 48 consistently annotated bird genomes spans 32 of the 35 recently proposed avian orders,* including all 30 neognath orders, and thus represents a wide range of avian evolutionary diversity. Our consortium's analyses have resulted in eight papers published today in Science, as well as 20 papers in other journals [avian.genomics.cn/en]. These include two flagship papers: one exploiting genomic-scale data to generate a highly supported avian order phylogeny that resolves many debates on the timing and topology of their radiation; the other a comparative genomic analysis exploring avian genome evolution and the genetic basis of complex traits. Other studies in Science describe convergent brain regions and gene expression for avian song learning and human speech, the singing activated genome in songbirds, complex evolutionary trajectories of avian sex chromosomes, a single loss of teeth in the ancestor of modern birds, the genomes of their closest extant outgroup (crocodilians) and inferred dinosaur ancestor, and computational methods developed for large-scale genomic analyses. Studies in companion papers explore the genomic adaptations of penguins, genomics of nearly extinct species, lineage-specific selection in birds, paleoviral infiltration in bird genomes, and many other questions. Thus, this study of a major vertebrate class highlights the future promise of large-scale comparative genomics, and we hope sets the stage for an approach for sequencing and analyses of many more genomes of birds and other vertebrate lineages. 

The placement of a strange South American bird called the hoatzin in the avian family tree is one of the many findings revealed this week from a massive international project analyzing the sequenced genomes of 48 bird species representing nearly every order of bird. The effort, involving 200 people from 80 labs and weeks of supercomputer time, has yielded the most definitive avian family tree yet. It has also pinpointed gene networks underlying the traits that make birds birds, such as feathers and beaks instead of teeth. In one provocative finding, a team has identified the gene network that underlies complex singing in birds—and found that the same network operates in humans, where it is presumably crucial to language. Already, 200 more bird genomes have been sequenced, with more waiting in the wings.