The genome of all birds

Birds live on all latitudes and on all continents. The discussion of their rapid evolution and amazing diversity lasts almost a century. Specialists have repeatedly built a phylogenetic tree of birds on the basis of the features of their anatomy, behavior and comparison of individual genes. The results, however, turned out to be contradictory.

The situation has changed when researchers have the opportunity to quickly secure whole genomes. The international group of scientists identified and compared the sequences of genomes of 48 species representing almost all the main detachments of the class of birds. DNA was distinguished from frozen samples provided by the Museum of the Natural History of the University of Louisian (USA), which has one of the world's largest collection of vertebrates.

The project was attended by more than 200 researchers from 80 institutions of 20 countries. He was headed by Guojie Zhang, Deputy Director of the National Genbank of the Beijing Institute of the Genoma and Associate Professor of Copenhagen University, Neurobiologist Eric Jarvis, employee of the University of Duc, and Professor Thomas Gilbert (M. Thomas P. Gilbert), an ancient DNA specialist working at the Danish Museum of Natural History.

The project took four years, including several months to go to computer analysis. Having done a huge work, scientists compiled a new phylogenetic tree of birds, restored the genome of their common ancestor and determined the genes responsible for the characteristic features of birds.

Fuck everything superfluous

The genome of birds is amazingly small. In mammals and reptiles, its dimensions vary from 1 to 8.2 GB, and in birds - from 0.91 GB in the ARCHILOCHUS ALEXANDERI beliber up to 1.3 GB at ostrich. The genome is small for several reasons. First of all, it has few repeated elements, only 4-10%, while mammals in their share are from 34 to 52%. The preserved bird repetitions are significantly shorter than that of other terrestrial vertebrates.

The birds shortened the intron, and as a result, the length of the genes encoding proteins, they have 50% and 27% less than in mammals and reptiles, respectively. Block mice, the only flying mammals, can boast of the same compact genome. Researchers suggested that condensed by the genome allows you to quickly regulate the operation of genes, which is beneficial during a controlled flight.

The genome was also reduced as a result of many large and small deeds (loss of fragments or removal of individual nucleotides). The formation of extended delections led, according to researchers, to fragmentation of chromosomes, due to which the genome of birds is replete with microchromosomes, this is its characteristic feature. A compact genome with a small number of repetitions, the low activity of mobile elements and microchromosomes was probably formed by the ancestors of birds and has been in this state for more than 100 million years.

The birds have lost many sequences that have been preserved in alligators and turtles, including 1241 coding gene, but they acquired several new signs. One of them is light, adapted for reinforced gas exchange during the flight. In mammals, lungs elastic, consisting of many alveoli, in birds they are small, dense and included in the running system of gas exchange (air enters both when inhale and when exhaled). Researchers discovered five genes that work in the formation of lungs in mammals, and there are no birds.

Another example is the loss of teeth. Instead, modern birds are used to grind the beak and muscular stomach. Most experts believe that the teeth have disappeared from a common ancestor of modern birds, while others believe that teeth loss could occur several times independently. At the same time, they refer to Hesperorinis and Ichthyorni-s-toothy birds of the mesozoic. To figure it out, the researchers compared the genomes of birds, turtles, which also do not have teeth, toothless mammals (Pangolins, ants and mustachioed whales) and mammals with teeth, devoid of enamel (pipes, sloths and armadillos).

All these vertebrates had ancestors with full -fledged enameled teeth, for the formation of which the “dentin” DSPP gene and five genes responsible for the formation of enamel ( ENAM , Amel , AMBN , MMP 20 and AMTN ) are needed. All toothless animals have genes encoding the formation of dentin and enamel as a result of mutations: deeds and shifts of the reading framework. Different species are different, but occurred in the same genes. In animals with teeth without enamel, only the DSPP gene works normally.

Analysis of mutations showed that the teeth disappeared by the ancestor of modern birds about 116 million years ago. At first, the teeth disappeared on the front of the upper and lower jaws, and the beak began to develop there. Then both processes spread to the back parts of both jaws. As a result, the keratinized beak successfully replaced his teeth and made a noticeable contribution to the formation of a variety of modern birds.

Tree of bird life

The main goal of the study of bird genomes and its main result was the construction of a consistent phylogenetic tree (see drawing). The existing classification, based on morphological studies and the results of the analysis of sequences of some chromosomal genes and mitochondrial DNA, divides modern birds (Neorniths) to Palaeognathae (non -altogething bloodless), Galloanseres, which include land -like Galliforems and water Guse -shaped Anserforms, and Neoaves - all other modern birds.

The NeoAVES group includes extensive treasures of water birds, including penguins, pelicans and gagars, and land birds (woodpeckers, birds of prey, parrots and singing birds). Despite the efforts of the systematic, the relations of branches inside Neoaves remained not entirely clear.

The new tree, based on the analysis of complete genomes, also distinguishes three groups, Palaeognathae, Galloanseres and Neoaves, and the last two are combined into the Neoognathae infralass (Novonebny). The first discrepancy inside Neoaves led to the formation of two monofiletic, that is, having one common ancestor, groups: Passerea, named after the most representative PasseriFormes group (sparrows), and Columbea, in honor of the squad of pigeons (Columbiformes). Inside, two large related treasures of land (Telluraves) and water (aequornithia) birds are distinguished inside the Passerea.

Among the lands, the Australves treasure is released, which includes the Cariam, traditionally related to crane -shaped (Gruiformes), falcons, which were usually placed with other daytime predators, parrots, the position of which on the tree difficult to determine, and sparrows. In another treasure, Afroaves entered among other eagles, owls, woodpeckers and rocket -like ones. Sokolov had to be separated from the eagles and vultures, and from the rakshamic detachment they excluded Kurolov and poultry.

As for the treasures of water birds, the researchers deduced the phaetons and sunlight from it. Their lifestyle is similar, but genomic differences do not allow combining these birds into one group. Scientists also found a place for birds, which were previously difficult to put on a certain branch: cuckoos, Turko and brefs. The Columbea treasure has its own surprises: pigeons and grouse turned out to be relatives of water birds, flamingos and repayables, which no one expected. Comparing the sequences of bird genomes with the genomes of the American alligator Alligator Mississippiensis , the crested crocodile CrocodyLus Porosus and the Indian gavial Gavialis gangeticus , scientists reconstructed the genome of birds and crocodiles, as well as the general genome The ancestor of the birds.

It turned out that the birds came from terrestrial vertebrates (therod) more than 150 million years ago, but their evolution accelerated the mass extinction of species that happened 66 million years ago and released many ecological niches. Few birds survived this disaster, but the surviving niches survived in just 10-15 million years, thanks to which they reached an amazing diversity. At the same time, placental mammals quickly evolved, they also did not miss their chance.

Having built a detailed, branched phylogenetic tree, the researchers got the opportunity to study the evolution of convergent features. Columbea and Passerea have many similar features that arose as a result of convergent evolution, and not because of close kinship. For example, when swimming underwater, the legs of the pollutions (columbea) work like a propeller, as well as that of Gagar and cormorants (Passerea). Flamingo (columbea) and the Ibisa and white herons related to Passerea feed in a similar way. But perhaps the most amazing example of convergence is singing.

Birds sing like people

The ability to sing arose in birds at least at least twice, or even three times: in hummingbirds and a common ancestor of parrots and singing birds. Some representatives of the Sparrow detachment have lost this ability, and the ProCnius Bellbirds call, which was not the singer, as it turned out, could learn how to sing.

By comparing the genomes of singing and not singing birds, the researchers discovered 227 genes associated with singing, most of which work in certain areas of the brain. These areas are active only in singing species. Scientists managed to decipher the mechanism of regulation of singing genes, the description of which they devoted a separate article.

The ability to simulate a song is characteristic not only by birds, but also by some mammals. Scientists compared the expression of genes in the brain of people, singing birds, parrots and hummingbirds, as well as birds and primates who do not sing: pigeons, quails and macaques.

It turned out that when singing, similar specialized proteins are synthesized in homologous areas of the brain of people and singing birds: these zones of the brain perform similar functions. The similarity between the regions located in the striatum (striped area) of the human brain and birds, which are activated in the process of speaking and singing, and between the areas of the back brain, responsible for the movement of the human larynx and the Sirinks (sound development in birds). It is amazing that such a convergence of the areas of the brain responsible for singing and speech, accompanied by convergent changes in the work of many genes, occurred in species divided at least 310 million years ago. Researchers suggest that for complex tasks there are a limited number of evolutionary solutions.

Window to evolution

Project participants have determined many genes that make a bird a bird. They found sequences responsible for the pneumatization of the bones of the skeleton, that is, the appearance of cavities filled with air in them; for the formation and coloring of the plumage; for beautiful color vision, thanks to which birds distinguish more shades than mammals; for the synthesis of digestive enzymes; For the loss of the right ovary (only the left is preserved in birds). They paid great attention to the evolution of sexual chromosomes, spermatogenesis and ovogenesis.

Researchers hope that the results they get will open a new window into evolution, the variety and environmental adaptation of ground vertebrates and help to make bridges between micro and macro-evolution. We will finish this engineering note, however, new results will not be long in coming, as scientists continue to secrete genomes of different types.

The results of the study are presented in 29 articles, 8 of which were included in the special production of Science (Science. 2014. Vol. 346. N 6215. P. 1261–1424), the rest in Genome Biology , Gigascience , BMC Journal and other publications. Full list of articles here: www.sciencemag.org/content/346/6215/1308/suppl/dc1