학술논문

Whole-genome analyses resolve early branches in the tree of life of modern birds
Document Type
article
Author
Jarvis, Erich DMirarab, SiavashAberer, Andre JLi, BoHoude, PeterLi, CaiHo, Simon YWFaircloth, Brant CNabholz, BenoitHoward, Jason TSuh, AlexanderWeber, Claudia Cda Fonseca, Rute RLi, JianwenZhang, FangLi, HuiZhou, LongNarula, NitishLiu, LiangGanapathy, GaneshBoussau, BastienBayzid, Md ShamsuzzohaZavidovych, VolodymyrSubramanian, SankarGabaldón, ToniCapella-Gutiérrez, SalvadorHuerta-Cepas, JaimeRekepalli, BhanuMunch, KasperSchierup, MikkelLindow, BentWarren, Wesley CRay, DavidGreen, Richard EBruford, Michael WZhan, XiangjiangDixon, AndrewLi, ShengbinLi, NingHuang, YinhuaDerryberry, Elizabeth PBertelsen, Mads FrostSheldon, Frederick HBrumfield, Robb TMello, Claudio VLovell, Peter VWirthlin, MorganSchneider, Maria Paula CruzProsdocimi, FranciscoSamaniego, José AlfredoVargas Velazquez, Amhed MissaelAlfaro-Núñez, AlonzoCampos, Paula FPetersen, BentSicheritz-Ponten, ThomasPas, AnBailey, TomScofield, PaulBunce, MichaelLambert, David MZhou, QiPerelman, PolinaDriskell, Amy CShapiro, BethXiong, ZijunZeng, YongliLiu, ShipingLi, ZhenyuLiu, BinghangWu, KuiXiao, JinYinqi, XiongZheng, QiuemeiZhang, YongYang, HuanmingWang, JianSmeds, LinneaRheindt, Frank EBraun, MichaelFjeldsa, JonOrlando, LudovicBarker, F KeithJønsson, Knud AndreasJohnson, WarrenKoepfli, Klaus-PeterO'Brien, StephenHaussler, DavidRyder, Oliver ARahbek, CarstenWillerslev, EskeGraves, Gary RGlenn, Travis CMcCormack, JohnBurt, DaveEllegren, HansAlström, PerEdwards, Scott VStamatakis, AlexandrosMindell, David PCracraft, Joel
Source
Science. 346(6215)
Subject
Human Genome
Genetics
Animals
Avian Proteins
Base Sequence
Biological Evolution
Birds
DNA Transposable Elements
Genes
Genetic Speciation
Genome
INDEL Mutation
Introns
Phylogeny
Sequence Analysis
DNA
General Science & Technology
Language
Abstract
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.