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AOU Classification Committee – North and Middle America
AOU Classification Committee – North and Middle America Proposal Set 2016-C No. Page Title 01 02 Change the English name of Alauda arvensis to Eurasian Skylark 02 06 Recognize Lilian’s Meadowlark Sturnella lilianae as a separate species from S. magna 03 20 Change the English name of Euplectes franciscanus to Northern Red Bishop 04 25 Transfer Sandhill Crane Grus canadensis to Antigone 05 29 Add Rufous-necked Wood-Rail Aramides axillaris to the U.S. list 06 31 Revise our higher-level linear sequence as follows: (a) Move Strigiformes to precede Trogoniformes; (b) Move Accipitriformes to precede Strigiformes; (c) Move Gaviiformes to precede Procellariiformes; (d) Move Eurypygiformes and Phaethontiformes to precede Gaviiformes; (e) Reverse the linear sequence of Podicipediformes and Phoenicopteriformes; (f) Move Pterocliformes and Columbiformes to follow Podicipediformes; (g) Move Cuculiformes, Caprimulgiformes, and Apodiformes to follow Columbiformes; and (h) Move Charadriiformes and Gruiformes to precede Eurypygiformes 07 45 Transfer Neocrex to Mustelirallus 08 48 (a) Split Ardenna from Puffinus, and (b) Revise the linear sequence of species of Ardenna 09 51 Separate Cathartiformes from Accipitriformes 10 58 Recognize Colibri cyanotus as a separate species from C. thalassinus 11 61 Change the English name “Brush-Finch” to “Brushfinch” 12 62 Change the English name of Ramphastos ambiguus 13 63 Split Plain Wren Cantorchilus modestus into three species 14 71 Recognize the genus Cercomacroides (Thamnophilidae) 15 74 Split Oceanodroma cheimomnestes and O. socorroensis from Leach’s Storm- Petrel O. leucorhoa 2016-C-1 N&MA Classification Committee p. 453 Change the English name of Alauda arvensis to Eurasian Skylark There are a dizzying number of larks (Alaudidae) worldwide and a first-time visitor to Africa or Mongolia might confront 10 or more species across several genera. -
Wqfm: Statistically Consistent Genome-Scale Species Tree Estimation from Weighted Quartets
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.30.403352; this version posted December 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. wQFM: Statistically Consistent Genome-scale Species Tree Estimation from Weighted Quartets Mahim Mahbub1;y, Zahin Wahab1;y, Rezwana Reaz1;y, M. Saifur Rahman1, and Md. Shamsuzzoha Bayzid1,* 1Department of Computer Science and Engineering Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh yThese authors contributed equally to this work *Corresponding author: shams [email protected] Abstract Motivation: Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incom- plete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collec- tion of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree allows for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging. Results: We propose wQFM, a highly accurate method for species tree es- timation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. -
Verbalizing Phylogenomic Conflict: Representation of Node Congruence Across Competing Reconstructions of the Neoavian Explosion
bioRxiv preprint doi: https://doi.org/10.1101/233973; this version posted December 14, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Tempe, December 12, 2017 RESEARCH ARTICLE (1st submission) Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion Nico M. Franz1*, Lukas J. Musher2, Joseph W. Brown3, Shizhuo Yu4, Bertram Ludäscher5 1 School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America 2 Richard Gilder Graduate School and Department of Ornithology, American Museum of Natural History, New York, New York, United States of America 3 Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom 4 Department of Computer Science, University of California at Davis, Davis, California, United States of America 5 School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America * Corresponding author E-mail: [email protected] Short title: Verbalizing phylogenomic conflict Abstract Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the novel products of phylogenomic inference – such as newly supported clade concepts – have not kept pace. However, the ability to verbalize both node concept congruence and conflict across multiple, (in effect) simultaneously endorsed phylogenomic hypotheses, is a critical prerequisite for building synthetic data environments for biological systematics, thereby also benefitting other domains impacted by these (conflicting) inferences. -
Data Types and the Phylogeny of Neoaves
Article Data Types and the Phylogeny of Neoaves Edward L. Braun * and Rebecca T. Kimball * Department of Biology, University of Florida, Gainesville, FL 32611, USA * Correspondence: ebraun68@ufl.edu (E.L.B.); rkimball@ufl.edu (R.T.K.) Simple Summary: Some of the earliest studies using molecular data to resolve evolutionary history separated birds into three main groups: Paleognathae (ostriches and allies), Galloanseres (ducks and chickens), and Neoaves (the remaining ~95% of avian species). The early evolution of Neoaves, however, has remained challenging to understand, even as data from whole genomes have become available. We have recently proposed that some of the conflicts among recent studies may be due to the type of genomic data that is analyzed (regions that code for proteins versus regions that do not). However, a rigorous examination of this hypothesis using coding and non-coding data from the same genomic regions sequenced from a relatively large number of species has not yet been conducted. Here we perform such an analysis and show that data type does influence the methods used to infer evolutionary relationships from molecular sequences. We also show that conducting analyses using models of sequence evolution that were chosen to minimize reconstruction errors result in coding and non-coding trees that are much more similar, and we add to the evidence that non-coding data provide better information regarding neoavian relationships. While a few relationships remain problematic, we are approaching a good understanding of the evolutionary history for major avian groups. Abstract: The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. -
Timing the Extant Avian Radiation: the Rise of Modern Birds, and The
1 Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation Daniel J. Field1, Jacob S. Berv2, Allison Y. Hsiang3, Robert Lanfear4, Michael J. Landis5, Alex Dornburg6 1 Department of Earth Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom 2Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA 3Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden 4Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia 5Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, USA 6 North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA Corresponding author: Daniel J. Field1 Email address: [email protected] PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.27521v1 | CC BY 4.0 Open Access | rec: 6 Feb 2019, publ: 6 Feb 2019 2 ABSTRACT Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary history (specifically, the interval immediately following the end-Cretaceous mass extinction). At face value this hypothesis enjoys support from the crown bird fossil record, which documents the first appearances of most major crown bird lineages in the early Cenozoic—in line with a model of rapid post-extinction niche filling among surviving avian lineages. However, molecular-clock analyses have yielded strikingly variable estimates for the age of crown birds, and conflicting inferences on the impact of the end-Cretaceous mass extinction on the extant bird radiation. -
A Taxonomic List of the Major Groups of Birds -With Indications of North American Families
A Taxonomic List of the Major Groups of Birds -with indications of North American families By David Lahti 2/2016 Following are the major groups of birds, as they have been designated so far, focusing especially on the Orders and Families of the current birds of the world, and designating (with underlines) families represented in North and Violet sabrewing Campylopterus Middle America. hemileucurus (Apodiformes: Trochilidae). Monteverde, Costa Rica (April Lahti, 2008). Avialans and extinct birds: A brief nested lineage is presented initially that starts with the Avialans—those dinosaurs believed to be more closely related to birds than to other dinos such as Deinonychus. Extinct fossil bird groups are presented mostly according to Chiappe (2001, 2002) and Sereno (2005). Until we get to modern birds (Neornithes), I have not represented groups as orders or families, because the most reliable paleontological data is still presented largely only at the level of genus. Some researchers (and researchers from some cultures in particlular) are apt to ascribe order status to their fossil finds, but it is very possible that nearly every genus discovered in the Jurassic and Cretaceous, at least, merits order status. Therefore I have avoided dividing genera into families and orders, and mentioned only the number of genera that have been described. Among modern birds, Neornithes, the vast majority of fossil and subfossil finds are thought to be consistent with contemporary orders; thus only four extinct orders are listed here, each designated by a dagger (†). Two of them (Lithornithiformes and Gastornithiformes) went extinct before the historical period, so are listed in the introductory ancient lineage; the other two (Dinornithiformes and Aepyornithiformes) went extinct in the historical period (because of humans), and so are in the main list. -
Phylogenetic Signal of Indels and the Neoavian Radiation
diversity Article Phylogenetic Signal of Indels and the Neoavian Radiation Peter Houde 1,*, Edward L. Braun 2,* , Nitish Narula 1 , Uriel Minjares 1 and Siavash Mirarab 3,* 1 Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA 2 Department of Biology, University of Florida, Gainesville, FL 32607, USA 3 Electrical and Computer Engineering, University of California, San Diego, CA 92093, USA * Correspondence: [email protected] (P.H.); ebraun68@ufl.edu (E.L.B.); [email protected] (S.M.); Tel.: +1-575-646-6019 (P.H.); +1-352-846-1124 (E.L.B.); +1-858-822-6245 (S.M.) Received: 3 June 2019; Accepted: 4 July 2019; Published: 6 July 2019 Abstract: The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. -
Prum Et Al Supplemental Materials Revision 9
SUPPLEMENTARY INFORMATION doi:10.1038/nature15697 A Comprehensive Phylogeny of Birds (Aves) using Targeted Next Generation DNA Sequencing Richard O. Prum1,2,*, Jacob S. Berv3,*, Alex Dornburg1,2,4, Daniel J. Field2,5, Jeffrey P. Townsend6, Emily Moriarty Lemmon7, and Alan R. Lemmon8 1 Department of Ecology & Evolutionary Biology, Yale University, New Haven CT USA 2 Peabody Museum of Natural History, Yale University, New Haven CT USA 3 Department of Ecology & Evolutionary Biology, Cornell University, Ithaca NY USA 4 North Carolina Museum of Natural Sciences, Raleigh NC USA 5 Department of Geology & Geophysics, Yale University, New Haven CT USA 6 Department of Biostatistics, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT USA 7 Department of Biological Science, Florida State University, Tallahassee, FL USA 8 Department of Scientific Computing, Florida State University, Tallahassee, FL USA * These authors contributed equally to this work. Online Data and Software Archive A zip archive containing assembled sequence data, newick formatted tree files, code and scripts for generating and analyzing phylogenetic informativeness, and information on probe design and data assembly is available at Zenodo.org: http://dx.doi.org/10.5281/zenodo.28343. R code used for generating tree and supplemental figures is available on request. Choosing Fossil Calibrations We elected to employ traditional node-based divergence dating instead of a fossil tip-dating approach1,2 due to the lack of a sufficiently extensive and reliable morphological data matrix for extant and fossil crown birds. Our node-dating approach followed the commonly employed method of specifying hard minimum bounds on the age of a divergence using fossils, while applying a ‘soft’ upper bound for date estimates3,4. -
Verbalizing Phylogenomic Conflict: Representation of Node Congruence Across Competing Reconstructions of the Neoavian Explosion
RESEARCH ARTICLE Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion 1 2 3 4 Nico M. FranzID *, Lukas J. MusherID , Joseph W. BrownID , Shizhuo Yu , Bertram LudaÈscher5 a1111111111 1 School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America, 2 Richard Gilder Graduate School and Department of Ornithology, American Museum of Natural History, New York, a1111111111 New York, United States of America, 3 Department of Animal and Plant Sciences, University of Sheffield, a1111111111 Sheffield, United Kingdom, 4 Department of Computer Science, University of California at Davis, Davis, a1111111111 California, United States of America, 5 School of Information Sciences, University of Illinois at Urbana- a1111111111 Champaign, Champaign, Illinois, United States of America * [email protected] OPEN ACCESS Abstract Citation: Franz NM, Musher LJ, Brown JW, Yu S, LudaÈscher B (2019) Verbalizing phylogenomic Phylogenomic research is accelerating the publication of landmark studies that aim to resolve conflict: Representation of node congruence deep divergences of major organismal groups. Meanwhile, systems for identifying and inte- across competing reconstructions of the neoavian grating the products of phylogenomic inference±such as newly supported clade concepts± explosion. PLoS Comput Biol 15(2): e1006493. have not kept pace. However, the ability to verbalize node concept congruence and conflict https://doi.org/10.1371/journal.pcbi.1006493 across -
Section 1. Systematics, Fossil Record, and Biogeography
SECTION 1. SYSTEMATICS, FOSSIL RECORD, AND BIOGEOGRAPHY Chapter 1 Pennaraptoran Systematics MICHAEL PITTMAN,1 JINGMAI O’CONNOR,2 DANIEL J. FIELD,3 ALAN H. TURNER,4 WAISUM MA,5 PETER MAKOVICKY,6 AND XING XU2 ABSTRACT New and important pennaraptoran specimens continue to be discovered on a regular basis. Yet, with these discoveries the number of viable phylogenetic hypotheses has increased, including ones that challenge the traditional grouping of dromaeosaurids and troodontids within a monophy- letic Deinonychosauria. This chapter will cover recent efforts to address prevailing phylogenetic uncertainties and controversies, both between and within key clades, including deinonychosaurian monophyly, the phylogenetic position of anchiornithines and scansoriopterygids, and the inter- relationships of enantiornithines. While recent discoveries mainly from Asia have created much of the latest uncertainty and controversy, new material, particularly from Asia, promises to rather fittingly address these issues. Further curatorship of long-standing phylogenetic datasets and more prevalent use of extended analytical protocols will be essential to meeting this challenge, especially for groups whose boundaries have been blurred. As it becomes increasingly difficult to study all fossil materials, owing to their growing numbers and ever disparate locations, broader use of digital fossils and online character databases for character coding is acutely needed to ensure that errors arising from remote, rather than firsthand, scoring are reduced as far as possible, particu- larly at this time of rapid data accumulation. 1 Vertebrate Palaeontology Laboratory, Division of Earth and Planetary Science, the University of Hong Kong, Hong Kong. 2 Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology & Paleoanthropology, Beijing; CAS Center for Excellence in Life and Paleoenvironment, Beijing. -
LETTER Doi:10.1038/Nature15697
LETTER doi:10.1038/nature15697 A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing Richard O. Prum1,2*, Jacob S. Berv3*, Alex Dornburg1,2,4, Daniel J. Field2,5, Jeffrey P. Townsend1,6, Emily Moriarty Lemmon7 & Alan R. Lemmon8 Although reconstruction of the phylogeny of living birds has pro- It has long been recognized that phylogenetic confidence depends gressed tremendously in the last decade, the evolutionary history of not only on the number of characters analysed and their rate of evolu- Neoaves—a clade that encompasses nearly all living bird species— tion, but also on the number and relationships of the taxa sampled remains the greatest unresolved challenge in dinosaur systematics. relative to the nodes of interest9–11. Theory predicts that sampling a Here we investigate avian phylogeny with an unprecedented scale single taxon that diverges close to a node of interest will have a far of data: .390,000 bases of genomic sequence data from each of greater effect on phylogenetic resolution than will adding more char- 198 species of living birds, representing all major avian lineages, acters11. Despite using an alignment of .40 million base pairs, sparse and two crocodilian outgroups. Sequence data were collected using sampling of 48 species in the recent avian genomic analysis may not anchored hybrid enrichment, yielding 259 nuclear loci with an have been sufficient to confidently resolve the deep divergences among average length of 1,523 bases for a total data set of over 7.8 3 107 major lineages of Neoaves. Thus, expanded taxon sampling is required bases. -
Prum Et Al. 2015
LETTER doi:10.1038/nature15697 A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing Richard O. Prum1,2*, Jacob S. Berv3*, Alex Dornburg1,2,4, Daniel J. Field2,5, Jeffrey P. Townsend1,6, Emily Moriarty Lemmon7 & Alan R. Lemmon8 Although reconstruction of the phylogeny of living birds has pro- It has long been recognized that phylogenetic confidence depends gressed tremendously in the last decade, the evolutionary history of not only on the number of characters analysed and their rate of evolu- Neoaves—a clade that encompasses nearly all living bird species— tion, but also on the number and relationships of the taxa sampled remains the greatest unresolved challenge in dinosaur systematics. relative to the nodes of interest9–11. Theory predicts that sampling a Here we investigate avian phylogeny with an unprecedented scale single taxon that diverges close to a node of interest will have a far of data: .390,000 bases of genomic sequence data from each of greater effect on phylogenetic resolution than will adding more char- 198 species of living birds, representing all major avian lineages, acters11. Despite using an alignment of .40 million base pairs, sparse and two crocodilian outgroups. Sequence data were collected using sampling of 48 species in the recent avian genomic analysis may not anchored hybrid enrichment, yielding 259 nuclear loci with an have been sufficient to confidently resolve the deep divergences among average length of 1,523 bases for a total data set of over 7.8 3 107 major lineages of Neoaves. Thus, expanded taxon sampling is required bases.