bird genomes
December 12, 2014

Groundbreaking Genetic Study Reveals Secrets Of Bird Evolution

Chuck Bednar for redOrbit.com - Your Universe Online

The secrets of how modern birds evolved and emerged following the mass extinction of the dinosaurs some 66 million years ago have long been hidden in their genes, but now an international team of more than 100 scientists has completed an extensive analysis of their DNA that has produced the most reliable tree of avian life ever.

The landmark study required the researchers to sequence, assemble and compare the full genomes of 48 bird species representing all major branches of modern birds, including the ostrich, hummingbird, crow, duck, falcon, parrot, crane, ibis, woodpecker and eagle species. This ambitious phylogeny project, which took four years to complete, has resulted in what is being hailed as the largest-ever whole genome study of a single class of animals.

Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, Erich D. Jarvis of Duke University and the Howard Hughes Medical Institute (HHMI), M. Thomas P. Gilbert of the Natural History Museum of Denmark and their colleagues are part of the Avian Phylogenomics Consortium, and they have published their results in 29 papers published this week – eight of them in a December 12 special edition of Science and 21 others in Genome Biology and other journals.

While scientists had already known that the birds who survived the mass extinction of the dinosaurs experienced a rapid evolutionary burst, the family tree of modern-day birds has long baffled biologists, as has the molecular details of how they managed to give rise to more than 10,000 known species. To solve some of those mysteries, the consortium members sequenced and analyzed the genomes of birds representing all major modern avian branches.

“Although an increasing number of vertebrate genomes are being released, to date no single study has deliberately targeted the full diversity of any major vertebrate group. This is precisely what our consortium set out to do,” said Gilbert. Jarvis called the findings “exciting,” adding “lots of fundamental questions now can be resolved with more genomic data from a broader sampling. I got into this project because of my interest in birds as a model for vocal learning and speech production in humans, and it has opened up some amazing new vistas on brain evolution.”

While this newly published research only represents the first form of genetic analysis, the study authors said that it presents some remarkable new information about avian evolution. One of the new flagship papers presents a well-resolved new family tree for birds that is based on whole-genome data, while a second details the overall genomic evolution of birds and others detail vocal learning, sex chromosomes, how birds lost their teeth and more.

“Previous attempts to reconstruct the avian family tree using partial DNA sequencing or anatomical and behavioral traits... met with contradiction and confusion,” Duke University's Kelly Rae Chi said in the statement. “Because modern birds split into species early and in such quick succession, they did not evolve enough distinct genetic differences at the genomic level to clearly determine their early branching order, the researchers said. To resolve the timing and relationships of modern birds, the consortium authors used whole-genome DNA sequences to infer the bird species tree.”

“In the past, people have been using 10 to 20 genes to try to infer the species relationships," Jarvis said. "What we've learned from doing this whole-genome approach is that we can infer a somewhat different phylogeny [family tree] than what has been proposed in the past. We've figured out that protein-coding genes tell the wrong story for inferring the species tree. You need non-coding sequences, including the intergenic regions. The protein coding sequences, however, tell an interesting story of proteome-wide convergence among species with similar life histories.”

One of the accomplishments of the new study is the resolution of the early branches of Neoaves (new birds), a group that represents approximately 95 percent of modern birds. These birds appeared somewhat suddenly, over the course of just a few million years, and the rapid appearance of so many species over such a short period of time made reconstructing their relationships far more difficult.

The whole-genome analysis, which involved computational analysis led by University of Illinois Founder Professor of Bioengineering and Computer Science Tandy Warnow and University of Texas at Austin graduate student Siavash Mirarab, dated the evolutionary expansion of Neoaves to the time of the mass extinction event 66 million years ago, contradicting the suggestion of recent research suggesting that these birds arose 10 to 80 million years earlier.

“Our results suggest that modern birds diversified in the wake of the mass extinction that marked the end of the age of dinosaurs, but we cannot exclude the possibility that birds began diversifying before the extinction,” co-author Edward Braun, a biology professor at the University of Florida, said in a statement. A total of 14,000 different regions within the genome of the 48 bird species were analyzed by the computational team, including both coding and non-coding sites in the genes.

Jane J. Lee of National Geographic called the research “embarrassment of scientific riches for studying everything from how birds evolved so quickly after dinosaurs disappeared to the ways in which birds and people learn.” She added that “the biggest takeaway” from the consortium’s research “is the way genetic codes can be used to answer wide-ranging questions. Scientists are using birds' DNA, for instance, both for research on the brain and learning and to reconstruct what an ancient ancestor of birds and dinosaurs might have looked like.”

She added that the study authors said that birds had an accelerated rate of evolution when compared to crocodilians and the common ancestors of both types of creatures, changing at rates similar to mammals but with genomes that were only about one-third the size. However, they all have the same basic functions as mammals, including the capacity for vocal learning, Texas Tech University biologist and study co-author David Ray told the National Geographic reporter.

Ray’s portion of the research started five years ago as an attempt to map one percent of crocodilian DNA, but expanded once the price of mapping a million bases reduced dramatically. Ultimately, they were able to sequence an entire genome of 3 billion bases. They found that the DNA in alligators, crocodiles and gharials is approximately 93 percent identical across the genome, or roughly equal to the DNA a human shares with a macaque.

The research also confirmed that birds and humans use essentially the same genes to speak. Jarvis and his Avian Phylogenomics Consortium colleagues found that vocal learning evolved at least twice and possibly three times in songbirds, parrots and hummingbirds, and that the set of genes involved in each of those adaptations is remarkably similar to the genes that give humans the ability to speak. Eight of the papers are devoted to bird songs, including one identifying 50 genes that show higher or lower activity in the brains of vocal learning birds and humans.

Despite the massive amount of research that has been published thus far, Professor David Burt, Acting Director of the National Avian Research Facility at the University of Edinburgh's Roslin Institute, said that this is “just the beginning. We hope that giving people the tools to explore this wealth of bird gene information in one place will stimulate further research. Ultimately, we hope the research will bring important insights to help improve the health and welfare of wild and farmed birds.”

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