DOCSLIB.ORG

LETTER Doi:10.1038/Nature15697

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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. Bayesian and maximum likelihood analyses yielded highly to test the monophyly of neoavian clades, and to further resolve the supported and nearly identical phylogenetic trees for all major phylogenetic relationships within Neoaves. avian lineages. Five major clades form successive sister groups to Here, we present a phylogenetic analysis of 198 bird species and the rest of Neoaves: (1) a clade including nightjars, other caprimul- 2 crocodilians (Supplementary Table 1) based on loci captured using giforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, anchored enrichment12. Our sample includes species of 122 avian bustards, and turacos with pigeons, mesites, and sandgrouse; (3) families in all 40 extant avian orders2, with denser representation of cranes and their relatives; (4) a comprehensive waterbird clade, non-oscine birds (108 families) than of oscine songbirds (14 families). including all diving, wading, and shorebirds; and (5) a compre- Effort was made to include taxa that would break up long phylogenetic hensive landbird clade with the enigmatic hoatzin (Opisthocomus branches, and provide the highest likelihood of resolving short inter- hoazin) as the sister group to the rest. Neither of the two main, nodes at the base of Neoaves11. We also sampled multiple species recently proposed Neoavian clades—Columbea and Passerea1— within groups whose monophyly or phylogenetic interrelationships were supported as monophyletic. The results of our divergence have been controversial—that is, tinamous, nightjars, hummingbirds, time analyses are congruent with the palaeontological record, sup- turacos, cuckoos, pigeons, sandgrouse, mesites, rails, storm petrels, porting a major radiation of crown birds in the wake of the petrels, storks, herons, hawks, hornbills, mousebirds, trogons, king- Cretaceous–Palaeogene (K–Pg) mass extinction. fishers, barbets, seriemas, falcons, parrots, and suboscine passerines. Birds (Aves) are the most diverse lineage of extant tetrapod verte- We targeted 394 loci centred on conserved anchor regions of the brates. They comprise over 10,000 living species2, and exhibit an extra- genome that are flanked by more variable regions12. We performed all ordinary diversity in morphology, ecology, and behaviour3. Substantial phylogenetic analyses on a data set of 259 genes with the highest progress has been made in resolving the phylogenetic history of birds. quality assemblies. The average locus was 1,524 bases in length Phylogenetic analyses of both molecular and morphological data sup- (361–2,316 base pairs (bp)), and the total percentage of missing data port the monophyletic Palaeognathae (the tinamous and flightless was 1.84%. The concatenated alignment contained 394,684 sites. To ratites) and Galloanserae (gamebirds and waterfowl) as successive, minimize overall model complexity while accurately accounting for monophyletic sister groups to the Neoaves—a diverse clade including substitution processes, we performed a partition model sensitivity all other living birds4. Resolving neoavian phylogeny has proven to be a analysis with PartitionFinder13,14, and compared a complex partition difficult challenge because this radiation was very rapid and deep in model (one partition per locus) to a heuristically optimized (rclust) time, resulting in very short internodes4. partition model. Phylogenetic informativeness (PI) approaches15,16 In the last decade, phylogenetic analyses of large, multilocus data provided strong evidence that the phylogenetic utility of our data set sets have resulted in the proposal of numerous, novel neoavian rela- was high, with low declines in PI profiles for individual loci, data set tionships. For example, a clade consisting of diving and wading birds partitions, and the concatenated matrix (Supplementary Fig. 4). We has been consistently recovered, as well as a large landbird clade in estimated concatenated trees in ExaBayes17 and RAxML18 using a 75 which falcons and parrots are successive sister groups to the perching partition model. Coalescent species trees were estimated with the gene birds4–8. Recently, phylogenetic analyses of 48 whole avian genomes tree summation methods in STAR19, NJst20, and ASTRAL21 from gene resulted in the proposal of a novel phylogenetic resolution of the initial trees estimated with RAxML (see Methods.) branching sequence within Neoaves1. Although this genomic study Our concatenated Bayesian analyses resulted in a completely provided much needed corroboration of many neoavian clades, the resolved, well supported phylogeny. All clades had a posterior prob- limited taxon sampling precluded further insights into the evolution- ability (PP) of 1, except for a single clade including shoebill ary history of birds. (Balaeniceps) and pelican (PP 5 0.54) (Fig. 1). The concatenated 1Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA. 2Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06520, USA. 3Department of Ecology and Evolutionary Biology, Fuller Evolutionary Biology Program, Cornell University, and Cornell Laboratory of Ornithology, Ithaca, New York 14853, USA. 4North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, USA. 5Department of Geology & Geophysics, Yale University, New Haven, Connecticut 06520, USA. 6Department of Biostatistics, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA. 7Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA. 8Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306, USA. *These authors contributed equally to this work. 00 MONTH 2015 | VOL 000 | NATURE | 1 G2015 Macmillan Publishers Limited. All rights reserved RESEARCH LETTER Aves 70 60 50 40 30 20 10 0 Ma Struthio Palaeognathae 190 Rhea 191 Apteryx 192 197 Casuarius Dromaius 193 Tinam. Tina 195 Eudromia 194 Nothoprocta am. 196 Crypturellus Tinamus Leipoa Galliformes 176 183 Ortalis Crax 177 Numida Galloanserae 178 182 Odontophorus Colinus 175 179 1 Rollulus 180 181 Bonasa Gallus Chauna Anseriform. 184 Anseranas 185 Dendrocygna 186 Oxyura 187 Anser 188 189 Anas Aythya Eurostopodus 173 174 Caprimulgus Chordeiles 163 Steatornis 172 Strisores Columbaves Gruiformes Aequorlitornithes 2 Nyctibius 164 Podargus 165 Aegotheles Hemiprocne Apodiform. 166 168 169 Streptoprocne 167 Chaetura 171 Topaza 170 Phaethornis Archilochus Otidimorph. 162 Tauraco Corythaeola 157 Ardeotis 158 Tapera 159 Centropus 160 161 Cuculus 3 148 Coccyzus Monias 156 Columbimorph. 154 Mesitornis 155 Syrrhaptes Pterocles 149 153 Ptilinopus Treron 150 Columbina 151 152 Leptotila Columba Heliornis 144 Neoaves Sarothrura 141 Rallus 142 143 Micropygia 140 Porphyrio Psophia 4 145 Aramus 146 147 Balearica Grus 139 Phoenicopterus Rollandia Burhinus 136 Charadrius 123 137 138 Haematopus Recurvirostra Pedionomus 124 132 133 Jacana 131 Rostratula Limosa 134 135 Arenaria 125 Tringa 98 Turnix 5 126 Glareola 127 Uria 128 Chroicocephalus 129 quorlitorn 130 Sterna Rynchops 122 Eurypyga Phaethon Gavia n nithes 99 Spheniscus 114 Phoebastria 115 121 Oceanites 100 Pelagodroma 116 Oceanodroma 117 Fulmarus 118 Puffinus 101 119 120 Pterodroma Pelecanoides 113 Ciconia 6 Leptoptilos Fregata 102 110 Morus 111 112 Anhinga 103 Phalacrocorax Theristicus Tigrisoma 104 106 107 Ardea 105 Ixobrychus Scopus 108 109 Balaeniceps Pelecanus Upper Palaeocene Eocene Oligocene Miocene Pli. Ple. Cretaceous Palaeogene Neogene Q. Figure 1 | Phylogeny of birds. Time-calibrated phylogeny of 198 species of sister clades are: Strisores (brown), Columbaves (purple), Gruiformes (yellow), birds inferred from a concatenated, Bayesian analysis of 259 anchored Aequorlitornithes (blue), and Inopinaves (green). Background colours mark phylogenomic loci using ExaBayes17. Figure continues on the opposite page geological periods. Ma, million years ago; Ple,
Load more

Recommended publications
  • Bakalářská Práce
    Univerzita Palackého v Olomouci Bakalářská práce Olomouc 2018 Monika Klaclová Univerzita Palackého v Olomouci Přírodovědecká fakulta Katedra botaniky Cross-species amplifikace mikrosatelitů z řádu tučňáci a konzervovaných ptačích mikrosatelitů u plameňáka růžového (Phoenicopterus roseus) Bakalářská práce Monika Klaclová Studijní program: Matematika Studijní obor: Matematika-Biologie Forma studia: Prezenční Olomouc 2018 Vedoucí práce: RNDr. Petr Nádvorník, Ph.D. Prohlašuji, že jsem tuto bakalářskou práci vypracovala samostatně pod vedením RNDr. Petra Nádvorníka, Ph.D. za použití uvedených literárních zdrojů. V Olomouci dne 27. 07. 2018 podpis: ............................ Monika Klaclová ii Srdečně děkuji vedoucímu bakalářské práce RNDr. Petru Nádvorníkovi, Ph.D. za věnovaný čas a odborné rady, které mi poskytl při zpracování této bakalářské práce. Dále děkuji kolektivu Laboratoře populační genetiky na Katedře buněčné biologie a genetiky Přírodovědecké fakulty Univerzity Palackého v Olomouci za zpříjemnění pracovního prostředí. iii Bibliografická identifikace Jméno a příjmení: Monika Klaclová Název práce: Cross-species amplifikace mikrosatelitů z řádu tučňáci a konzervovaných ptačích mikrosatelitů u plameňáka růžového (Phoenicopterus roseus) Typ práce: Bakalářská práce Pracoviště: Katedra buněčné biologie a genetiky, Přírodovědecká fakulta Univerzity Palackého v Olomouci Vedoucí práce: RNDr. Petr Nádvorník, Ph.D. Rok obhajoby: 2018 Abstrakt V této bakalářské práci jsem se zabývala hledáním polymorfních mikrosatelitů u plameňáka růžového
    [Show full text]
  • A Comprehensive Multilocus Phylogeny of the Neotropical Cotingas
    Molecular Phylogenetics and Evolution 81 (2014) 120–136 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A comprehensive multilocus phylogeny of the Neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification ⇑ Jacob S. Berv 1, Richard O. Prum Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, P.O. Box 208105, New Haven, CT 06520, USA article info abstract Article history: The Neotropical cotingas (Cotingidae: Aves) are a group of passerine birds that are characterized by Received 18 April 2014 extreme diversity in morphology, ecology, breeding system, and behavior. Here, we present a compre- Revised 24 July 2014 hensive phylogeny of the Neotropical cotingas based on six nuclear and mitochondrial loci (7500 bp) Accepted 6 September 2014 for a sample of 61 cotinga species in all 25 genera, and 22 species of suboscine outgroups. Our taxon sam- Available online 16 September 2014 ple more than doubles the number of cotinga species studied in previous analyses, and allows us to test the monophyly of the cotingas as well as their intrageneric relationships with high resolution. We ana- Keywords: lyze our genetic data using a Bayesian species tree method, and concatenated Bayesian and maximum Phylogenetics likelihood methods, and present a highly supported phylogenetic hypothesis. We confirm the monophyly Bayesian inference Species-tree of the cotingas, and present the first phylogenetic evidence for the relationships of Phibalura flavirostris as Sexual selection the sister group to Ampelion and Doliornis, and the paraphyly of Lipaugus with respect to Tijuca.
    [Show full text]
  • Dieter Thomas Tietze Editor How They Arise, Modify and Vanish
    Fascinating Life Sciences Dieter Thomas Tietze Editor Bird Species How They Arise, Modify and Vanish Fascinating Life Sciences This interdisciplinary series brings together the most essential and captivating topics in the life sciences. They range from the plant sciences to zoology, from the microbiome to macrobiome, and from basic biology to biotechnology. The series not only highlights fascinating research; it also discusses major challenges associated with the life sciences and related disciplines and outlines future research directions. Individual volumes provide in-depth information, are richly illustrated with photographs, illustrations, and maps, and feature suggestions for further reading or glossaries where appropriate. Interested researchers in all areas of the life sciences, as well as biology enthusiasts, will find the series’ interdisciplinary focus and highly readable volumes especially appealing. More information about this series at http://www.springer.com/series/15408 Dieter Thomas Tietze Editor Bird Species How They Arise, Modify and Vanish Editor Dieter Thomas Tietze Natural History Museum Basel Basel, Switzerland ISSN 2509-6745 ISSN 2509-6753 (electronic) Fascinating Life Sciences ISBN 978-3-319-91688-0 ISBN 978-3-319-91689-7 (eBook) https://doi.org/10.1007/978-3-319-91689-7 Library of Congress Control Number: 2018948152 © The Editor(s) (if applicable) and The Author(s) 2018. This book is an open access publication. Open Access This book is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.
    [Show full text]
  • 1 Integrative Biology 200 "PRINCIPLES OF
    Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler March 14, 2018. Classification II: Phylogenetic taxonomy including incorporation of fossils; PhyloCode I. Phylogenetic Taxonomy - the argument for rank-free classification A number of recent calls have been made for the reformation of the Linnaean hierarchy (e.g., De Queiroz & Gauthier, 1992). These authors have emphasized that the existing system is based in a non-evolutionary world-view; the roots of the Linnaean hierarchy are in a specially- created world-view. Perhaps the idea of fixed, comparable ranks made some sense under that view, but under an evolutionary world view they don't make sense. There are several problems with the current nomenclatorial system: 1. The current system, with its single type for a name, cannot be used to precisely name a clade. E.g., you may name a family based on a certain type specimen, and even if you were clear about what node you meant to name in your original publication, the exact phylogenetic application of your name would not be clear subsequently, after new clades are added. 2. There are not nearly enough ranks to name the thousands of levels of monophyletic groups in the tree of life. Therefore people are increasingly using informal rank-free names for higher- level nodes, but without any clear, formal specification of what clade is meant. 3. Most aspects of the current code, including priority, revolve around the ranks, which leads to instability of usage. For example, when a change in relationships is discovered, several names often need to be changed to adjust, including those of groups whose circumscription has not changed.
    [Show full text]
  • Another Darwinian Aesthetics
    This is a repository copy of Another Darwinian Aesthetics. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/103826/ Version: Accepted Version Article: Wilson, Catherine orcid.org/0000-0002-0760-4072 (2016) Another Darwinian Aesthetics. Journal of aesthetics and art criticism. pp. 237-252. ISSN 0021-8529 https://doi.org/10.1111/jaac.12283 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Another Darwinian Aesthetics (Last ms version). Published Version: WILSON, CATHERINE. "Another Darwinian Aesthetics." The Journal of Aesthetics and Art Criticism 74.3 (2016): 237-252. Despite the bright sun, dew was still dripping from the chrysanthemums in the garden. On the bamboo fences, and criss-cross hedges, I saw tatters of spiderwebs; and where the threads were broken the raindrops hung on them like strings of white pearls. I was greatly moved and delighted. …Later I described to people how beautiful it all was.
    [Show full text]
  • Current Perspectives on Sexual Selection History, Philosophy and Theory of the Life Sciences Volume 9
    Current Perspectives on Sexual Selection History, Philosophy and Theory of the Life Sciences Volume 9 Editors: Charles T. Wolfe, Ghent University, Belgium Philippe Huneman, IHPST (CNRS/Université Paris I Panthéon-Sorbonne), France Thomas A.C. Reydon, Leibniz Universität Hannover, Germany Editorial Board: Editors Charles T. Wolfe, Ghent University, Belgium Philippe Huneman, IHPST (CNRS/Université Paris I Panthéon-Sorbonne), France Thomas A.C. Reydon, Leibniz Universität Hannover, Germany Editorial Board Marshall Abrams (University of Alabama at Birmingham) Andre Ariew (Missouri) Minus van Baalen (UPMC, Paris) Domenico Bertoloni Meli (Indiana) Richard Burian (Virginia Tech) Pietro Corsi (EHESS, Paris) François Duchesneau (Université de Montréal) John Dupré (Exeter) Paul Farber (Oregon State) Lisa Gannett (Saint Mary’s University, Halifax) Andy Gardner (Oxford) Paul Griffi ths (Sydney) Jean Gayon (IHPST, Paris) Guido Giglioni (Warburg Institute, London) Thomas Heams (INRA, AgroParisTech, Paris) James Lennox (Pittsburgh) Annick Lesne (CNRS, UPMC, Paris) Tim Lewens (Cambridge) Edouard Machery (Pittsburgh) Alexandre Métraux (Archives Poincaré, Nancy) Hans Metz (Leiden) Roberta Millstein (Davis) Staffan Müller-Wille (Exeter) Dominic Murphy (Sydney) François Munoz (Université Montpellier 2) Stuart Newman (New York Medical College) Frederik Nijhout (Duke) Samir Okasha (Bristol) Susan Oyama (CUNY) Kevin Padian (Berkeley) David Queller (Washington University, St Louis) Stéphane Schmitt (SPHERE, CNRS, Paris) Phillip Sloan (Notre Dame) Jacqueline Sullivan
    [Show full text]
  • Reading: Masters of Light: the Science Behind Nature's Brightest
    Masters of Light: The Science Behind Nature’s Brightest Colors JULIA ROTHCHILD DECEMBER 30, 2014 0 In the sands of the Yukon Territory in Canada, a scientist found a beetle embedded with nano-scale diamonds. The insect was a small, brown member of the weevil family. It was plated with hollow scales, inside each of which expanses of nano-crystals had grown. Every diamond was placed exactly the same distance apart, yielding a formidably regular array that extended up and down and side to side, filling the insides of the beetle’s scales with a rigid, repeating matrix. The insect unearthed in the Yukon sand had been preserved for over half a million years as a fossil. Yale researchers inspected the preserved material using high energy X-rays at Argonne National Laboratory in Chicago in order to study the configuration of crystals. Although the structures they discovered are especially beautiful and intriguing, diamond-filled scales are not unique: many creatures alive today grow identical or similar nano-size arrays. Animals grow these sorts of structures because they are optical powerhouses. By manipulating light, the crystals allow animals to produce brilliant colors that are otherwise unattainable. Making Blue Consider the color blue. There are no blue bears in the world. There are no blue crocodiles either. There are also no blue kangaroos, blue bumblebees, blue cats, or blue dogs. There aren’t very many blue animals in the world, period, because blue is a difficult color to make. Most of the other colors of the rainbow arise straightforwardly in nature from chemicals, called pigments, that animals collect in their skin, feathers, and hair.
    [Show full text]
  • 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.
    [Show full text]
  • Crown Clades in Vertebrate Nomenclature
    2008 POINTS OF VIEW 173 Wiens, J. J. 2001. Character analysis in morphological phylogenetics: Wilkins, A. S. 2002. The evolution of developmental pathways. Sinauer Problems and solutions. Syst. Biol. 50:689–699. Associates, Sunderland, Massachusetts. Wiens, J. J., and R. E. Etheridge. 2003. Phylogenetic relationships of Wright, S. 1934a. An analysis of variability in the number of digits in hoplocercid lizards: Coding and combining meristic, morphometric, an inbred strain of guinea pigs. Genetics 19:506–536. and polymorphic data using step matrices. Herpetologica 59:375– Wright, S. 1934b. The results of crosses between inbred strains 398. of guinea pigs differing in number of digits. Genetics 19:537– Wiens, J. J., and M. R. Servedio. 1997. Accuracy of phylogenetic analysis 551. including and excluding polymorphic characters. Syst. Biol. 46:332– 345. Wiens, J. J., and M. R. Servedio. 1998. Phylogenetic analysis and in- First submitted 28 June 2007; reviews returned 10 September 2007; traspecific variation: Performance of parsimony, likelihood, and dis- final acceptance 18 October 2007 tance methods. Syst. Biol. 47:228–253. Associate Editor: Norman MacLeod Syst. Biol. 57(1):173–181, 2008 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150801910469 Crown Clades in Vertebrate Nomenclature: Correcting the Definition of Crocodylia JEREMY E. MARTIN1 AND MICHAEL J. BENTON2 1UniversiteL´ yon 1, UMR 5125 PEPS CNRS, 2, rue Dubois 69622 Villeurbanne, France; E-mail: [email protected] 2Department of Earth Sciences, University of Bristol, Bristol, BS9 1RJ, UK; E-mail: [email protected] Downloaded By: [Martin, Jeremy E.] At: 19:32 25 February 2008 Acrown group is defined as the most recent common Dyke, 2002; Forey, 2002; Monsch, 2005; Rieppel, 2006) ancestor of at least two extant groups and all its descen- but rather expresses dissatisfaction with the increasingly dants (Gauthier, 1986).
    [Show full text]
  • 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.
    [Show full text]
  • Interspecific Social Dominance Mimicry in Birds
    bs_bs_banner Zoological Journal of the Linnean Society, 2014. With 6 figures Interspecific social dominance mimicry in birds RICHARD OWEN PRUM1,2* 1Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8150, USA 2Peabody Natural History Museum, Yale University, New Haven, CT 06520-8150, USA Received 3 May 2014; revised 17 June 2014; accepted for publication 21 July 2014 Interspecific social dominance mimicry (ISDM) is a proposed form of social parasitism in which a subordinate species evolves to mimic and deceive a dominant ecological competitor in order to avoid attack by the dominant, model species. The evolutionary plausibility of ISDM has been established previously by the Hairy-Downy game (Prum & Samuelson). Psychophysical models of avian visual acuity support the plausibility of visual ISDM at distances ∼>2–3 m for non-raptorial birds, and ∼>20 m for raptors. Fifty phylogenetically independent examples of avian ISDM involving 60 model and 93 mimic species, subspecies, and morphs from 30 families are proposed and reviewed. Patterns of size differences, phylogeny, and coevolutionary radiation generally support the predic- tions of ISDM. Mimics average 56–58% of the body mass of the proposed model species. Mimics may achieve a large potential deceptive social advantage with <20% reduction in linear body size, which is well within the range of plausible, visual size confusion. Several, multispecies mimicry complexes are proposed (e.g. kiskadee- type flycatchers) which may coevolve through hierarchical variation in the deceptive benefits, similar to Müllerian mimicry. ISDM in birds should be tested further with phylogenetic, ecological, and experimental investigations of convergent similarity in appearance, ecological competition, and aggressive social interactions between sympatric species.
    [Show full text]
  • 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.
    [Show full text]