Bigger better bird tree of life will soon fly into view

first_img By Elizabeth PennisiApr. 16, 2018 , 2:35 PM Email A better family tree would help researchers better place turacos, such as this Knysna turaco from South Africa, on its branches. Click to view the privacy policy. Required fields are indicated by an asterisk (*) Bigger, better bird tree of life will soon fly into view Daniel J. Field center_img Sign up for our daily newsletter Get more great content like this delivered right to you! Country Country * Afghanistan Aland Islands Albania Algeria Andorra Angola Anguilla Antarctica Antigua and Barbuda Argentina Armenia Aruba Australia Austria Azerbaijan Bahamas Bahrain Bangladesh Barbados Belarus Belgium Belize Benin Bermuda Bhutan Bolivia, Plurinational State of Bonaire, Sint Eustatius and Saba Bosnia and Herzegovina Botswana Bouvet Island Brazil British Indian Ocean Territory Brunei Darussalam Bulgaria Burkina Faso Burundi Cambodia Cameroon Canada Cape Verde Cayman Islands Central African Republic Chad Chile China Christmas Island Cocos (Keeling) Islands Colombia Comoros Congo Congo, the Democratic Republic of the Cook Islands Costa Rica Cote d’Ivoire Croatia Cuba Curaçao Cyprus Czech Republic Denmark Djibouti Dominica Dominican Republic Ecuador Egypt El Salvador Equatorial Guinea Eritrea Estonia Ethiopia Falkland Islands (Malvinas) Faroe Islands Fiji Finland France French Guiana French Polynesia French Southern Territories Gabon Gambia Georgia Germany Ghana Gibraltar Greece Greenland Grenada Guadeloupe Guatemala Guernsey Guinea Guinea-Bissau Guyana Haiti Heard Island and McDonald Islands Holy See (Vatican City State) Honduras Hungary Iceland India Indonesia Iran, Islamic Republic of Iraq Ireland Isle of Man Israel Italy Jamaica Japan Jersey Jordan Kazakhstan Kenya Kiribati Korea, Democratic People’s Republic of Korea, Republic of Kuwait Kyrgyzstan Lao People’s Democratic Republic Latvia Lebanon Lesotho Liberia Libyan Arab Jamahiriya Liechtenstein Lithuania Luxembourg Macao Macedonia, the former Yugoslav Republic of Madagascar Malawi Malaysia Maldives Mali Malta Martinique Mauritania Mauritius Mayotte Mexico Moldova, Republic of Monaco Mongolia Montenegro Montserrat Morocco Mozambique Myanmar Namibia Nauru Nepal Netherlands New Caledonia New Zealand Nicaragua Niger Nigeria Niue Norfolk Island Norway Oman Pakistan Palestine Panama Papua New Guinea Paraguay Peru Philippines Pitcairn Poland Portugal Qatar Reunion Romania Russian Federation Rwanda Saint Barthélemy Saint Helena, Ascension and Tristan da Cunha Saint Kitts and Nevis Saint Lucia Saint Martin (French part) Saint Pierre and Miquelon Saint Vincent and the Grenadines Samoa San Marino Sao Tome and Principe Saudi Arabia Senegal Serbia Seychelles Sierra Leone Singapore Sint Maarten (Dutch part) Slovakia Slovenia Solomon Islands Somalia South Africa South Georgia and the South Sandwich Islands South Sudan Spain Sri Lanka Sudan Suriname Svalbard and Jan Mayen Swaziland Sweden Switzerland Syrian Arab Republic Taiwan Tajikistan Tanzania, United Republic of Thailand Timor-Leste Togo Tokelau Tonga Trinidad and Tobago Tunisia Turkey Turkmenistan Turks and Caicos Islands Tuvalu Uganda Ukraine United Arab Emirates United Kingdom United States Uruguay Uzbekistan Vanuatu Venezuela, Bolivarian Republic of Vietnam Virgin Islands, British Wallis and Futuna Western Sahara Yemen Zambia Zimbabwe Bird lovers—and evolutionary biologists—can look forward to a new and improved avian family tree being finished in 4 years, thanks to The OpenWings Project officially launched this last week at the American Ornithological Meeting in Tucson, Arizona. The $1.42 million effort will be the first to include DNA data from the more than 10,500 known bird species to establish how they are all related. But it will not be the final word—another project seeking to sequence the full genomes of every avian species will follow if enough funding can be raised. OpenWings “will be a huge improvement over what we have now,” says Harvard University evolutionary biologist Scott Edwards. But, “Ultimately, OpenWings will be a stepping stone to the grand tree that the whole genomes [will generate].”  In 2014, biologists published an avian tree based on the sequences of whole genomes of about 40 species. Another team published a different tree in 2015 after comparing a subset of the avian genome in hundreds of species. These phylogenies help researchers looking at the evolutionary histories of specific avian traits or the story of birds overall. But some researchers who specialize in building trees were not satisfied. “The current need for large phylogenies and the high priority placed on them by high impact journals can result in shortcuts, wherein large-scale phylogenetic trees are cobbled together from disparate existing sources, even taxonomy, but often without hard data behind the placement of many species,” Harvard evolutionary biologist Gustavo Bravo and his colleagues wrote on 30 January in PeerJ. “The question is how far do you compromise?” Edwards adds.So even though some of the leaders of the 2014 avian tree effort launched the Bird 10,000 Genomes (B10K) Project, aiming to eventually sequence the whole genomes of all 10,560 bird species and from there build “the grand tree,” some bird researchers decided not to wait. Led by Brian Smith at the American Museum of Natural History in New York City and Brant Faircloth at Louisiana State University in Baton Rouge, they are taking a cheaper, faster route with the OpenWings Project. The U.S. National Science Foundation–funded effort will tap extensive museum collections as much as possible, instead of freshly caught bird samples, and will sequence about 5000 short pieces of the DNA, focusing on regions that are very highly conserved among all birds. The group plans to release data on an ongoing basis, rather than waiting for the project’s publication, so other researchers can make use of it. The OpenWings tree will give “us a better understanding of the process of [bird] diversification and can potentially give us the information we need to move forward in understanding vertebrate diversification,” Faircloth says.But how good a tree will it be? “I don’t think [OpenWings] is going to solve well enough their goal of generating an accurate tree, says B10K leader Erich Jarvis, a neurogenomicist at The Rockefeller University in New York City. In the 2014 work, he and his colleagues compared trees built from just the conserved DNA regions OpenWings will also examine to those arising from whole-genome comparisons and found inaccuracies in the former. He argues that whole genomes will not only provide more data for building trees, but will also enable researchers to study the evolution of regulatory sequences, transposable elements, and other aspects of the genome that are not covered with OpenWings sequencing. Once a genome is finished, no more sequencing of that species’s DNA will be ever needed, he argues.Jarvis worries that OpenWings will dampen enthusiasm and slow support for B10K, which could cost up to $150 million for high quality, so-called reference genomes, and still isn’t fully funded. Furthermore, Jarvis is concerned about using up rare samples. Some birds, such as species endemic to Borneo, are very hard to find and collect, and there’s a chance the two projects may wind up competing for DNA from the few samples gathered. Edwards does not think that’s a big problem, however, and says B10K needs better DNA than can be retrieved from the museums specimens that OpenWings plans to use. Faircloth hopes his team will not use any of the samples used in the B10K project, as having DNA sequence from multiple individuals of the same species can be useful. With help from the Chinese sequencing giant BGI, B10K has already sequenced to some degree the genomes of more than 300 birds, with representatives for each family and subfamily. But additional support is required to go much further, Jarvis says. “I don’t want people to get the impression that once OpenWings is finished that we are finished [with bird DNA studies],” he adds.last_img read more