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Neognathae

About: Neognathae is a research topic. Over the lifetime, 38 publications have been published within this topic receiving 5688 citations. The topic is also known as: neognaths.

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Journal ArticleDOI
27 Jun 2008-Science
TL;DR: This study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods.
Abstract: Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

1,833 citations

Journal ArticleDOI
Erich D. Jarvis1, Siavash Mirarab2, Andre J. Aberer3, Bo Li4, Bo Li5, Bo Li6, Peter Houde7, Cai Li6, Cai Li5, Simon Y. W. Ho8, Brant C. Faircloth9, Benoit Nabholz, Jason T. Howard1, Alexander Suh10, Claudia C. Weber10, Rute R. da Fonseca11, Jianwen Li, Fang Zhang Zhang, Hui Li, Long Zhou, Nitish Narula12, Nitish Narula7, Liang Liu13, Ganesh Ganapathy1, Bastien Boussau, Shamsuzzoha Bayzid2, Volodymyr Zavidovych1, Sankar Subramanian14, Toni Gabaldón15, Salvador Capella-Gutierrez, Jaime Huerta-Cepas, Bhanu Rekepalli16, Bhanu Rekepalli17, Kasper Munch18, Mikkel H. Schierup18, Bent E. K. Lindow11, Wesley C. Warren19, David A. Ray, Richard E. Green20, Michael William Bruford21, Xiangjiang Zhan22, Xiangjiang Zhan21, Andrew Dixon, Shengbin Li4, Ning Li23, Yinhua Huang23, Elizabeth P. Derryberry24, Elizabeth P. Derryberry25, Mads F. Bertelsen26, Frederick H. Sheldon24, Robb T. Brumfield24, Claudio V. Mello27, Claudio V. Mello28, Peter V. Lovell28, Morgan Wirthlin28, Maria Paula Cruz Schneider27, Francisco Prosdocimi27, José Alfredo Samaniego11, Amhed Missael Vargas Velazquez11, Alonzo Alfaro-Núñez11, Paula F. Campos11, Bent O. Petersen29, Thomas Sicheritz-Pontén29, An Pas, Thomas L. Bailey, R. Paul Scofield30, Michael Bunce31, David M. Lambert14, Qi Zhou, Polina L. Perelman32, Amy C. Driskell33, Beth Shapiro20, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Quiemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnéa Smeds10, Frank E. Rheindt34, Michael J. Braun35, Jon Fjeldså11, Ludovic Orlando11, F. Keith Barker6, Knud A. Jønsson6, Warren E. Johnson33, Klaus-Peter Koepfli33, Stephen J. O'Brien36, David Haussler, Oliver A. Ryder, Carsten Rahbek6, Eske Willerslev11, Gary R. Graves33, Gary R. Graves6, Travis C. Glenn13, John E. McCormack37, Dave Burt38, Hans Ellegren10, Per Alström, Scott V. Edwards39, Alexandros Stamatakis3, David P. Mindell40, Joel Cracraft6, Edward L. Braun41, Tandy Warnow42, Tandy Warnow2, Wang Jun, M. Thomas P. Gilbert31, M. Thomas P. Gilbert6, Guojie Zhang11, Guojie Zhang5 
12 Dec 2014-Science
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
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.

1,624 citations

Journal ArticleDOI
22 Oct 2015-Nature
TL;DR: The results of the divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.
Abstract: Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades--Columbea and Passerea--were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.

1,094 citations

Journal ArticleDOI
TL;DR: The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary, and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.
Abstract: Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

631 citations

Journal ArticleDOI
TL;DR: It is shown that avian colour vision shifted between VS and UVS at least 14 times, and single nucleotide substitutions can explain all these shifts.
Abstract: Colour vision in birds can be categorized into two classes, the ultraviolet (UVS) and violet sensitive (VS) Their phylogenetic distributions have traditionally been regarded as highly conserved However, the complicated nature of acquiring spectral sensitivities from cone photoreceptors meant that until recently, only a few species had actually been studied Whether birds are UVS or VS can nowadays be inferred from a wide range of species via genomic sequencing of the UV/violet SWS1 cone opsin gene We present genomic sequencing results of the SWS1 gene from 21 avian orders Amino acid residues signifying UV sensitivity are found in the two most important spectral tuning sites 86 and 90 of Pteroclidiformes and Coraciiformes, in addition to the major clades, Palaeognathae, Charadriiformes, Trogoniformes, Psittaciformes and Passeriformes, where they where previously known to occur We confirm that the presumed UVS-conferring amino acid combination F86, C90 and M93 is common to Palaeognathae and unique to this clade, despite available spectrometric evidence showing the ostrich retina to be VS By mapping our results together with data from previous studies on a molecular phylogeny we show that avian colour vision shifted between VS and UVS at least 14 times Single nucleotide substitutions can explain all these shifts The common ancestor of birds most likely had a VS phenotype However, the ancestral state of the avian SWS1 opsin’s spectral tuning sites cannot be resolved, since the Palaeognathae are F86, C90 while the Neognathae are ancestrally S86, S90 The phylogenetic distribution of UVS and VS colour vision in birds is so complex that inferences of spectral sensitivities from closely related taxa should be used with caution

135 citations

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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20213
20201
20191
20181
20172
20153