A Model of Avian Genome Evolution
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Understanding the Building Blocks of Avian Complex Cognition : The
Understanding the building blocks of avian complex cognition: the executive caudal nidopallium and the neuronal energy budget by Kaya von Eugen A thesis submitted in partial fulfilment of the requirements for the degree of Philosophiae Doctoris (PhD) in Neuroscience From the International Graduate School of Neuroscience Ruhr University Bochum September 30th 2020 This research was conducted at the Department of Biopsychology, within the Faculty of Psychology at the Ruhr University under the supervision of Prof. Dr. Dr. h.c. Onur Güntürkün Printed with the permission of the International Graduate School of Neuroscience, Ruhr University Bochum Statement I certify herewith that the dissertation included here was completed and written independently by me and without outside assistance. References to the work and theories of others have been cited and acknowledged completely and correctly. The “Guidelines for Good Scientific Practice” according to § 9, Sec. 3 of the PhD regulations of the International Graduate School of Neuroscience were adhered to. This work has never been submitted in this, or a similar form, at this or any other domestic or foreign institution of higher learning as a dissertation. The abovementioned statement was made as a solemn declaration. I conscientiously believe and state it to be true and declare that it is of the same legal significance and value as if it were made under oath. Bochum, 30.09.2020 Kaya von Eugen PhD Commission Chair: PD Dr. Dirk Jancke 1st Internal Examiner: Prof. Dr. Dr. h.c. Onur Güntürkün 2nd Internal Examiner: Prof. Dr. Carsten Theiß External Examiner: Prof. Dr. Andrew Iwaniuk Non-Specialist: Prof. -
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. -
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. -
Asynchronous Evolution of Interdependent Nest Characters Across the Avian Phylogeny
ARTICLE DOI: 10.1038/s41467-018-04265-x OPEN Asynchronous evolution of interdependent nest characters across the avian phylogeny Yi-Ting Fang1, Mao-Ning Tuanmu 2 & Chih-Ming Hung 2 Nest building is a widespread behavior among birds that reflects their adaptation to the environment and evolutionary history. However, it remains unclear how nests evolve and how their evolution relates to the bird phylogeny. Here, by examining the evolution of three nest — — 1234567890():,; characters structure, site, and attachment across all bird families, we reveal that nest characters did not change synchronically across the avian phylogeny but had disparate evolutionary trajectories. Nest structure shows stronger phylogenetic signal than nest site, while nest attachment has little variation. Nevertheless, the three characters evolved inter- dependently. For example, the ability of birds to explore new nest sites might depend on the emergence of novel nest structure and/or attachment. Our results also reveal labile nest characters in passerines compared with other birds. This study provides important insights into avian nest evolution and suggests potential associations between nest diversification and the adaptive radiations that generated modern bird lineages. 1 Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan. 2 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. Correspondence and requests for materials should be addressed to M.-N.T. (email: [email protected]) or to C.-M.H. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:1863 | DOI: 10.1038/s41467-018-04265-x | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04265-x lmost all birds build nests, ranging from a simple scratch attachment. -
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. -
Coos, Booms, and Hoots: the Evolution of Closed-Mouth Vocal Behavior in Birds
ORIGINAL ARTICLE doi:10.1111/evo.12988 Coos, booms, and hoots: The evolution of closed-mouth vocal behavior in birds Tobias Riede, 1,2 Chad M. Eliason, 3 Edward H. Miller, 4 Franz Goller, 5 and Julia A. Clarke 3 1Department of Physiology, Midwestern University, Glendale, Arizona 85308 2E-mail: [email protected] 3Department of Geological Sciences, The University of Texas at Austin, Texas 78712 4Department of Biology, Memorial University, St. John’s, Newfoundland and Labrador A1B 3X9, Canada 5Department of Biology, University of Utah, Salt Lake City 84112, Utah Received January 11, 2016 Accepted June 13, 2016 Most birds vocalize with an open beak, but vocalization with a closed beak into an inflating cavity occurs in territorial or courtship displays in disparate species throughout birds. Closed-mouth vocalizations generate resonance conditions that favor low-frequency sounds. By contrast, open-mouth vocalizations cover a wider frequency range. Here we describe closed-mouth vocalizations of birds from functional and morphological perspectives and assess the distribution of closed-mouth vocalizations in birds and related outgroups. Ancestral-state optimizations of body size and vocal behavior indicate that closed-mouth vocalizations are unlikely to be ancestral in birds and have evolved independently at least 16 times within Aves, predominantly in large-bodied lineages. Closed-mouth vocalizations are rare in the small-bodied passerines. In light of these results and body size trends in nonavian dinosaurs, we suggest that the capacity for closed-mouth vocalization was present in at least some extinct nonavian dinosaurs. As in birds, this behavior may have been limited to sexually selected vocal displays, and hence would have co-occurred with open-mouthed vocalizations. -
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. -
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. -
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. -
Rapid Laurasian Diversification of a Pantropical Bird Family During The
Ibis (2020), 162, 137–152 doi: 10.1111/ibi.12707 Rapid Laurasian diversification of a pantropical bird family during the Oligocene–Miocene transition CARL H. OLIVEROS,1,2* MICHAEL J. ANDERSEN,3 PETER A. HOSNER,4,7 WILLIAM M. MAUCK III,5,6 FREDERICK H. SHELDON,2 JOEL CRACRAFT5 & ROBERT G. MOYLE1 1Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA 2Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 3Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA 4Division of Birds, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, USA 5Department of Ornithology, American Museum of Natural History, New York, NY, USA 6New York Genome Center, New York, NY, USA 7Natural History Museum of Denmark and Center for Macroecology, Evolution, and Climate; University of Copenhagen, Copenhagen, Denmark Disjunct, pantropical distributions are a common pattern among avian lineages, but dis- entangling multiple scenarios that can produce them requires accurate estimates of his- torical relationships and timescales. Here, we clarify the biogeographical history of the pantropical avian family of trogons (Trogonidae) by re-examining their phylogenetic rela- tionships and divergence times with genome-scale data. We estimated trogon phylogeny by analysing thousands of ultraconserved element (UCE) loci from all extant trogon gen- era with concatenation and coalescent approaches. We then estimated a time frame for trogon diversification using MCMCTree and fossil calibrations, after which we performed ancestral area estimation using BioGeoBEARS. We recovered the first well-resolved hypothesis of relationships among trogon genera. -
Phthiraptera: Ischnocera: Philopteridae) on Sandpipers (Aves: Charadriiformes: Scolopacidae)
Systematic Entomology (2017), 42, 509–522 DOI: 10.1111/syen.12227 Unexpected distribution patterns of Carduiceps feather lice (Phthiraptera: Ischnocera: Philopteridae) on sandpipers (Aves: Charadriiformes: Scolopacidae) DANIEL R. GUSTAFSSON1 andURBAN OLSSON2 1Department of Biology, University of Utah, Salt Lake City, UT, U.S.A. and 2Systematics and Biodiversity, Department of Zoology, University of Gothenburg, Gothenburg, Sweden Abstract. The louse genus Carduiceps Clay & Meinertzhagen, 1939 is widely distributed on sandpipers and stints (Calidrinae). The current taxonomy includes three species on the Calidrinae (Carduiceps meinertzhageni, Carduiceps scalaris, Carduiceps zonarius) and four species on noncalidrine hosts. We estimated a phylogeny of four of the seven species of Carduiceps (the three mentioned above and Carduiceps fulvofasciatus) from 13 of the 29 hosts based on three mitochondrial loci, and evaluated the relative importance of flyway differentiation (same host species has different lice along different flyways) and flyway homogenization (different host species have the same lice along the same flyway). We found no evidence for either process. Instead, the present, morphology-based, taxonomy of the genus corresponds exactly to the gene-based phylogeny, with all four included species monophyletic. Carduiceps zonarius is found both to inhabit a wider range of hosts than wing lice of the genus Lunaceps occurring on the same group of birds, and to occur on Calidris sandpipers of all sizes, both of which are unexpected for a body louse. The previously proposed family Esthiopteridae is found to be monophyletic with good support. The concatenated dataset suggests that the pigeon louse genus Columbicola may be closely related to the auk and diver louse genus Craspedonirmus. -
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.