Nrem4464exam1-19KEY

Total Page:16

File Type:pdf, Size:1020Kb

Nrem4464exam1-19KEY NREM/BIOL 4464 1 MARCH 2019 O’CONNELL ORNITHOLOGY EXAM 1 In full compliance with University policy on Academic Integrity, my signature below is my pledge that I will neither seek nor provide information during this examination that would confer a prohibited advantage in performance to myself or any other student. I fully understand that if I am found in violation of this standard that the minimum punishment for said violation would be a grade of zero for this examination. Signature: ANSWER KEY Printed name: _____________________________ MULTIPLE CHOICE (1 pt. eaCh) CirCle the letter corresponding with best response. 1) Pennaceous feathers consist of a long central shaft from which branching filaments extend. Those filaments attached directly to that central shaft are called . a) barbs. d) remiges. b) barbules. e) hooklets. c) calamuses. 2) Surveys for the North American Breeding Bird Survey are conducted during which months? a) March–April c) July–August b) May–June d) September–October 3) On what level of biological organization does natural selection act? a) individual c) species b) population d) down low 4) Two closely related species are morphologically distinct, but will occasionally pair and produce apparently healthy hybrid offspring. Life history studies of those offspring, however, indicate that they are almost invariably infertile. Which one of the following terms best describes this scenario? a) genetic bottleneck d) positive assortative mating b) adaptive radiation e) None of the above accurately describes the c) post-mating reproduCtive isolating meChanism scenario. 5) The Lacey Act (1900) specifically outlawed what practice in the US? a) fastening shoes with buckles d) the tailoring of any clothing without frilly ruffs b) acting or lacey appliqués c) trade in illegally obtained wildlife parts 6) The National Wildlife Federation’s highest honor, the ______________ Award, is named in honor of a game warden killed by poachers while trying to protect nesting wading birds in Florida in 1905. a) Jordan Peele c) Ariana Grande b) Guy Bradley d) Michael Cohen 7) Which one of the following statements most accurately reflects the conclusions of the Zink et al. (2010) study of microsatellites and mitochondrial dNA in Black-capped Vireo? a) Genetic relatedness was high among c) Genetic relatedness was high among populations in Oklahoma and Texas, but the populations in Mexico and Oklahoma, but the Mexican population was distinct. Texas population was distinct. b) Genetic relatedness was high among d) There was some evidence of genetiC variability populations in Mexico and Texas, but the among the three populations, but it was not Oklahoma population was distinct. struCtured geographiCally. 1 8) The nine-volume American Ornithology published between 1808 and 1814 was written by . a) John James Audubon. c) Peter Griffin. b) Mark Catesby. d) Alexander Wilson. 9) Which one of the following naturalists published The Birds of Oklahoma in 1931, bore 5 children and published papers in childhood development on them, spoke at least 5 languages, pretty much founded the modern study of behavioral ecology, and was the first female president of the Wilson Ornithological Society and elected fellow of the American Ornithologists’ Union? a) Charles darwin d) Charles darwin b) Margaret Morse NiCe e) John James Audubon c) Roger Tory Peterson 10) Among the citizen science monitoring programs we have discussed in class, which one would be the best source for information on the wintering distribution of Red-tailed Hawk from 1950–1980? a) Christmas Bird Count c) Great Backyard Bird Count b) eBird d) Breeding Bird Survey 11) In the evolutionary history of birds from theropod dinosaurs, what is the significance of Anchiornis relative to Archaeopteryx? a) Anchiornis appears to have been insectivorous. d) Anchiornis appears in the fossil reCord millions of b) Anchiornis had a long, bony tail, quite unlike years before Archaeopteryx. Archaeopteryx. e) Archaeopteryx was black and gray but Anchiornis c) Anchiornis had a crest but Archaeopteryx did not. had blue patches in its wings. 12) Which one of the following is NOT a synapomorphy among most modern birds, Archaeopteryx, and maniraptors (e.g., Velociraptor)? a) feathers d) semi-lunate carpal b) bladelike scapula e) massive keel on the sternum c) high metabolism 13) Why is the Great Backyard Bird Count of particular relevance to the conservation of Harris’s Sparrow? a) Harris’s Sparrow only occurs in great backyards. c) Harris’s Sparrow breeds in the ArCtiC where it is not b) Harris’s Sparrow often comes to feeders after a snow detected well by other monitoring programs. or ice storm. d) Harris’s Sparrow migrates through the Great Plains. 14) Of the 32 Neognathous orders of modern birds, 22 of those orders are further grouped into the . a) galloanseres. c) tinamous (tinamiformes). b) columbea. d) passerea. FILL-IN DEFINITIONS (2 pts. eaCh) 15. SPECIATION: the splitting of one evolutionary lineage into two or more. 16. PHENETICS: field of study that classifies species solely according to their overall physical similarity to other species. 17. SYNAPOMORPHIES: shared, derived characters that are weighted heavily in a cladistic analysis. 2 18. POLYMORPHISM: two or more discrete phenotypes in a sympatric population. 19. PTERYLAE: feather tracts, i.e., specific regions from which feathers grow on the skin of most birds. 20. MICROSATELLITES: repeated sequences of 1–6 base pairs of dNA. These sequences have high mutation rates resulting in many polymorphisms that can indicate genetic diversity within populations of the same species. SHORT ANSWER 21. Of the 8 modifications of the AXIAL skeleton in birds compared to ancestral reptiles, e.g., Cotylosaurs, list any 4. (Note: Be not vague! If you think some modification of the tail has occurred, then describe that modification. You will get no credit for simply writing the word “tail”.) (4 pts) Axial skeleton Includes skull, all vertebrae (cervical, dorsal {thoracic, lumbar}, sacral and caudal), ribCage, and sternum. *Secondary bony palate *Hingelike ankle - no lateral movement *3-fingered hand, 4-toed foot *High metabolism *Semi-lunate carpal *Big eyes, big brains *Furcula *FEATHERS! *Bladelike scapula 22. Of the 9 functions of feathers that have nothing to do with flight (flight is the 10th), list any 4 and provide an example of each. (Again, be not vague.) (4 pts) Feather functions: •insulation (e.g., nestlings) •waterproofing (e.g., Common Loon) •crypsis (e.g., owls, nestlings) •display (e.g., general display of health and vigor: •flight pink color of Greater Flamingo) •species/gender recognition (e.g., sexually •Gathering food (e.g., rictal bristles) dimorphic species like Red-winged Blackbird) •Gathering water (e.g., modified belly feathers of •special display (e.g., modified feathers of Club- sandgrouse) winged Manakin, Marvelous Spatuletail) •Perch prop (e.g., woodpeckers) 23. There are three groups of vertebrates (besides flying fish!) that independently evolved powered flight. What are those three groups of organisms? discuss the analogous and homologous structures in these groups that power their flight. (6 pts – please write out this answer in complete sentences.) Powered flight arose independently among the birds, pterosaurs, and the bats. In these groups, their wings are analogous structures, because the flying membrane is unique to each group: feathers supported by the arm in birds, skin supported by the hand in bats, and skin supported one enormous digit in the pterosaurs. The bones of the arm and hand, however, are homologous among all three groups: humerus, radius, ulna, carpals, metacarpals, and phalanges can be found in each group. 3 24. The following cladogram of a hypothetical taxon includes species a–l. Draw a line around any polyphyletic group on this cladogram. What criterion identifies your group as polyphyletic? Provide an example of a real- life polyphyletic group, and why it is polyphyletic. (6 pts – please write out this answer in complete sentences.) d e g h k l C f j b a A polyphyletic group does not arise from a single, common ancestor. In the example above, h and k are polyphyletic as a taxon because their grouping does not include their immediate common ancestors of a. In fact, h and k have different immediate ancestors that are not in the taxon. Polyphyletic taxa have their place: flowering plants and mosses arose from different common ancestors, so any kingdom of plants that includes mosses and flowering plants is a polyphyletic grouping, not a monophyletic one. Thus, recognition of plants as a kingdom is not in keeping with a cladistic approach to systematics, but we still find it useful as both groups are sessile, conduct photosynthesis, etc. Among birds, the old order Falconiformes we now know to be polyphyletic because genomic sequencing has revealed that falcons are not closely related to hawks, eagles, etc. Total Points: _____46______/40 (46 possible!) 4 .
Recommended publications
  • Dense Sampling of Bird Diversity Increases Power of Comparative Genomics
    Article Dense sampling of bird diversity increases power of comparative genomics https://doi.org/10.1038/s41586-020-2873-9 A list of authors and affiliations appears at the end of the paper. Received: 9 August 2019 Whole-genome sequencing projects are increasingly populating the tree of life and Accepted: 27 July 2020 characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed Published online: 11 November 2020 to confound phylogenetic inference5, and captures only a fraction of the genomic Open access diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird Check for updates families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confdently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specifc variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will ofer new perspectives on evolutionary processes in cross-species comparative analyses and assist in eforts to conserve species.
    [Show full text]
  • Prezentace Aplikace Powerpoint
    PTÁCI 1.část Systém ptáků Systém ptáků -zatím stále velmi nestabilní Passerimorphae - Psittaciformes, Passeriformes Falconiformes - Coliiformes, Trogoniformes, Coraciimorphae Bucerotiformes, Strigiformes Piciformes, Coraciiformes Accipitrimorphae - Accipitriformes - Pelecaniformes Suliformes Pelecanimorphae Ciconiiformes Procellariimorphae - Sphenisciformes, Procellariiformes Gaviimorphae - Gaviiformes Phaethontimorphae Cursorimorphae - Gruiformes, Charadriiformes Passerea Opisthocomiformes - Caprimulgiformes, Neoaves Caprimulgimorphae Apodiformes - Cuculiformes, Musophagifomes, Otidimorphae Otidiformes Columbimorphae - Columbiformes, Pterocliformes, Columbea Mesitornithiformes Phoenicopterimorphae - Podicipediformes, Phoenicopteriformes PTÁCI • opeření, přední končetiny- křídla, kostrční žláza • pneumatizace kostí, heterocélní obratle • bipední pohyb (palec dozadu, ostatní prsty dopředu) • srůsty kostí, srůsty na lebce, zobák (ramfotéka) • srůst klíčních kostí (furcula) • zvětšení koncového mozku, zdokonalení oka a ucha • malé plíce se vzdušnými vaky, endotermie • vejce s vápenitou skořápkou, péče o mláďata Avifauna ČR • dnes známo asi 10 000 druhů (druhá nejpočetnější „třída“) • u nás 403 druhů ptáků (k 12.12.2018) • u nás asi 200 hnízdících druhů • Česká společnost ornitologická (www.birdlife.cz) Létaví - Neognathae Řád: HRABAVÍ (Galliformes) - zavalití ptáci, pozemní (ale spí na větvích) - noha anizodaktylní (kráčivá), silná – hrabavá, silné tupé drápy, často ostruha - krátký zobák, na hlavě časté kožené výrůstky - pohlaví často odlišně
    [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]
  • ECDC/EFSA Joint Report: Avian Influenza Overview October
    SCIENTIFIC REPORT APPROVED: 29 September 2017 doi: 10.2903/j.efsa.2017.5018 Avian influenza overview October 2016–August 2017 European Food Safety Authority, European Centre for Disease Prevention and Control, European Union Reference Laboratory for Avian influenza, Ian Brown, Paolo Mulatti, Krzysztof Smietanka, Christoph Staubach, Preben Willeberg, Cornelia Adlhoch, Denise Candiani, Chiara Fabris, Gabriele Zancanaro, Joana Morgado and Frank Verdonck Abstract The A(H5N8) highly pathogenic avian influenza (HPAI) epidemic occurred in 29 European countries in 2016/2017 and has been the largest ever recorded in the EU in terms of number of poultry outbreaks, geographical extent and number of dead wild birds. Multiple primary incursions temporally related with all major poultry sectors affected but secondary spread was most commonly associated with domestic waterfowl species. A massive effort of all the affected EU Member States (MSs) allowed a descriptive epidemiological overview of the cases in poultry, captive birds and wild birds, providing also information on measures applied at the individual MS level. Data on poultry population structure are required to facilitate data and risk factor analysis, hence to strengthen science-based advice to risk managers. It is suggested to promote common understanding and application of definitions related to control activities and their reporting across MSs. Despite a large number of human exposures to infected poultry occurred during the ongoing outbreaks, no transmission to humans has been identified. Monitoring the avian influenza (AI) situation in other continents indicated a potential risk of long-distance spread of HPAI virus (HPAIV) A(H5N6) from Asia to wintering grounds towards Western Europe, similarly to what happened with HPAIV A(H5N8) and HPAIV A(H5N1) in previous years.
    [Show full text]
  • 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.
    [Show full text]
  • Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds Erich D
    AFLOCKOFGENOMES 90. J. F. Storz, J. C. Opazo, F. G. Hoffmann, Mol. Phylogenet. Evol. RESEARCH ARTICLE 66, 469–478 (2013). 91. F. G. Hoffmann, J. F. Storz, T. A. Gorr, J. C. Opazo, Mol. Biol. Evol. 27, 1126–1138 (2010). Whole-genome analyses resolve ACKNOWLEDGMENTS Genome assemblies and annotations of avian genomes in this study are available on the avian phylogenomics website early branches in the tree of life (http://phybirds.genomics.org.cn), GigaDB (http://dx.doi.org/ 10.5524/101000), National Center for Biotechnology Information (NCBI), and ENSEMBL (NCBI and Ensembl accession numbers of modern birds are provided in table S2). The majority of this study was supported by an internal funding from BGI. In addition, G.Z. was 1 2 3 4,5,6 7 supported by a Marie Curie International Incoming Fellowship Erich D. Jarvis, *† Siavash Mirarab, * Andre J. Aberer, Bo Li, Peter Houde, grant (300837); M.T.P.G. was supported by a Danish National Cai Li,4,6 Simon Y. W. Ho,8 Brant C. Faircloth,9,10 Benoit Nabholz,11 Research Foundation grant (DNRF94) and a Lundbeck Foundation Jason T. Howard,1 Alexander Suh,12 Claudia C. Weber,12 Rute R. da Fonseca,6 grant (R52-A5062); C.L. and Q.L. were partially supported by a 4 4 4 4 7,13 14 Danish Council for Independent Research Grant (10-081390); Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, and E.D.J. was supported by the Howard Hughes Medical Institute Ganesh Ganapathy,1 Bastien Boussau,15 Md.
    [Show full text]
  • Global Diversity of Birds 2015
    Ornithology NREM/ZOOL 4464 Dr. Tim O’Connell Spring 2015 A Classification of Birds of the World – Laboratory Investigations As students of Ornithology, a primary objective for you is to develop a working knowledge of the diversity of birds of the world. As you internalize this information, you will develop a deep appreciation for the central role that evolution plays as the driver of biological diversity. We begin this week in Lab to really explore the diversity of birds through in-depth examination of orders and families. Avian classification is fluid: the ordering and alliance of families and orders differs according to different authorities and new information is continually becoming available that enhances our ability to discern relationships; this results in updated classifications. You are embarking on this voyage during a time of significant taxonomic revision, and much of what you will learn in Lab supersedes classification systems in your field guides. Different authorities (usually committees) often disagree in their assessment of a taxon. Where one authority might recognize a full species, another might recognize it as a subspecies of some other species. Higher-level assignments are tricky too, e.g., some place the South American rheas in their own order (Rheiformes) whereas others lump it in with other ostrich-like birds in Struthioniformes. The American Ornithologists’ Union manages two committees (North American and South American Classification Committees) that review information and render decisions on which taxonomic proposals will be recognized. Each July, the AOU publishes updates to its official checklist. That checklist is commonly accessed via a massive book containing information on distribution, evolutionary affinities, etc.
    [Show full text]
  • Istoria Critica a Romanilortj
    7i4-aftrtuy,c,,J.LT(19t.tt IllCOF-F7-- ,,,Akt=tym=11:=1,10.40==i° \ P. ID_ HAS DM-U. ISTORIA CRITICA A ROMANILORTJ 4. 16 14, pAATEN TULLT TERRET-ROMANESCI VOLUMULU I. 3 INTINDEREA TERRITORIALA. NOMENCLATURA. ACTIUNEA NAT-RE ID I 'T I IT 1\7" E.A II REVEpUTi BSI FORTE ADAUSA r1 .AeXCrAzEUGeko PRETULt VOLUMULUI: 24 lei noui. Depositil Ia autorit: Callea MogoOia ur. 172. B U C U R E S C I TYPOGRAPHIA THIEL & WEISS C STRADA LIPSCANI No. 11- 13. I 8 7 4. 0,1 or 1/4 ArROF ,.) ,w I-1 .A_ S ID M -CT ,...V......P.e..0...W. ISTORIA CRITICA A ROMANILORU 33_ P.. 1-1.A_SDMIT ISTORIA CRITICA A ROMANILORU PAMENTULU TERREI-110MANESCI voLunuLt I. INTINDEREA TERRITORIALA. NOMENCLATORA. ACTIUNEA NATURE 1. BUCURESCI IMPRIMERIA STATULUI No. 2. STRADA GERMANA, No. 2. 1 8 7 5. MEMORIEI REPOS A.TULUI MEU PARINTE SI MAGISTRU IN SCIINTA ISTORICA ALESSANDRIT PETRICEICU- HASDEtI, ALLE SELLE DINTRE ALLE SELLE, DEDICU ACESTU ANTEIU VOLUDIU Copilluld, se mica fart ast6mpord din instinctiva pornire de a'qi intari nascondavi- gore prin gimnastica. Giunele se increde orbesce in tad ce'l esse inainte, caci alts -felid n'ara c4tiga recea ispita cu pretuld desamagirii. Sossesce apoi o vresta candy omula, matura la corpa, hi anima §i la minte, se con- centra in sine, devenindu elln insuo o mica lume, basata in relatiunile selle cu lumea cea mare pe principiuld conservatiunii §i desvoltarii individuale. Alasunt §i pop:Vele. Pruncialora se manifests printr'o sgomotOsa dinamica; tincretea, prin velleitatt fe- derative; barbatia, prin nationalisms.
    [Show full text]
  • Avian Genomics : Fledging Into the Wild!
    Erschienen in: Journal of Ornithology ; 156 (2015), 4. - S. 851-865 https://dx.doi.org/10.1007/s10336-015-1253-y Avian genomics: fledging into the wild! Robert H. S. Kraus1,2 • Michael Wink3 Abstract Next generation sequencing (NGS) technolo- Zusammenfassung gies provide great resources to study bird evolution and avian functional genomics. They also allow for the iden- Die Ornithologie ist im Zeitalter der Genomik ange- tification of suitable high-resolution markers for detailed kommen analyses of the phylogeography of a species or the con- nectivity of migrating birds between breeding and winter- Neue Sequenziertechnologien (Next Generation Sequen- ing populations. This review discusses the application of cing; NGS) ero¨ffnen die Mo¨glichkeit, Evolution und DNA markers for the study of systematics and phylogeny, funktionelle Genomik bei Vo¨geln umfassend zu untersu- but also population genetics and phylogeography. chen. Weiterhin erlaubt die NGS-Technologie, geeignete, Emphasis in this review is on the new methodology of hochauflo¨sende Markersysteme fu¨r Mikrosatelliten und NGS and its use to study avian genomics. The recent Single Nucleotide Polymorphisms (SNPs) zu identifizieren, publication of the first phylogenomic tree of birds based on um detaillierte Analysen zur Phylogeographie einer Art genome data of 48 bird taxa from 34 orders is presented in oder zur Konnektivita¨t von Zugvo¨geln zwischen Brut- und more detail. Winterpopulationen durchzufu¨hren. Dieses Review widmet sich der Anwendung von DNA Markern fu¨r die Erfor- Keywords Next generation sequencing Á Genetics Á schung von Systematik und Phylogenie sowie Populati- Ornithology Á Whole genome Á Phylogenomics Á Single onsgenetik und Phylogeographie.
    [Show full text]
  • The Origin and Diversification of Birds
    Current Biology Review The Origin and Diversification of Birds Stephen L. Brusatte1,*, Jingmai K. O’Connor2,*, and Erich D. Jarvis3,4,* 1School of GeoSciences, University of Edinburgh, Grant Institute, King’s Buildings, James Hutton Road, Edinburgh EH9 3FE, UK 2Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China 3Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA 4Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA *Correspondence: [email protected] (S.L.B.), [email protected] (J.K.O.), [email protected] (E.D.J.) http://dx.doi.org/10.1016/j.cub.2015.08.003 Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two de- cades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and became so successful. Birds evolved from theropod dino- saurs during the Jurassic (around 165–150 million years ago) and their classic small, lightweight, feathered, and winged body plan was pieced together gradually over tens of millions of years of evolution rather than in one burst of innovation. Early birds diversified throughout the Jurassic and Cretaceous, becoming capable fliers with supercharged growth rates, but were decimated at the end-Cretaceous extinction alongside their close dinosaurian relatives. After the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today. Introduction dinosaurs Dromaeosaurus albertensis or Troodon formosus.This Birds are one of the most conspicuous groups of animals in the clade includes all living birds and extinct taxa, such as Archaeop- modern world.
    [Show full text]
  • 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.
    [Show full text]
  • And Effective Population Size
    1/25/2019 Lineage Sorting is a function of time (in Coalescent analyses of genome-scale indel (insertion- generations) and deletion) data provide a unique source of information effective population about avian species tree and ancestral population sizes size (Ne) Edward Braun - University of Florida smaller populations tend to Peter Houde & Nitish Narula - New Mexico State University have more recent common Siavash Mirarab - University of California San Diego ancestors PAG, January 2019 Preview Probability of concordance with species tree For a rooted three-taxon species tree the probability that a gene Background tree matches the species tree is simple: −푡 Indel data 2 2푁e 푃 = 1 − 3 Estimating species trees with indels (Pamilo and Nei 1988 Mol Biol Evol 5:568-583) Avian demography at the K-Pg boundary Where P is the probability that a gene tree matches the species tree, t is the internal branch length (in generations), and Ne is the effective population size Lineage Sorting Hemiplasy Evidence of Hemiplasy and ILS - Time-dependent process - Alleles can have evolutionary by which species lose histories that differ from the ancestral polymorphissm species tree Incongruent gene trees - Result of incomplete lineage through via genetic drift - problem: apparent gene tree incongruence can result sorting (ILS) from incorrect gene phylogenies (will cause the amount ancestral of incongruence to be overestimated) polymorphism ancestral polymorphism the shorter the time Incongruent genetic markers, e.g., transposable elements complete between speciations, - problem: too few and unequally distributed to be free of the more ILS, sampling artifacts complete the more complete hemiplasy Indels improve on these shortcomings because they are a very large data set with limited true homoplasy Robinson et al 2008 PNAS 105:14477-14481 1 1/25/2019 Jarvis et al 2014 Insertion/Deletion (Indel) Data Set1 Available estimates… (from Jarvis et al.
    [Show full text]