Feather Evolution from Precocial to Altricial Birds
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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 -
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. -
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. -
A Model of Avian Genome Evolution
bioRxiv preprint doi: https://doi.org/10.1101/034710; this version posted April 30, 2016. 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. A Model of Avian Genome Evolution LiaoFu LUO Faculty of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China email: [email protected] Abstract Based on the reconstruction of evolutionary tree for avian genome a model of genome evolution is proposed. The importance of k-mer frequency in determining the character divergence among avian species is demonstrated. The classical evolutionary equation is written in terms of nucleotide frequencies of the genome varying in time. The evolution is described by a second-order differential equation. The diversity and the environmental potential play dominant role on the genome evolution. Environmental potential parameters, evolutionary inertial parameter and dissipation parameter are estimated by avian genomic data. To describe the speciation event the quantum evolutionary equation is proposed which is the generalization of the classical equation through correspondence principle. The Schrodinger wave function is the probability amplitude of nucleotide frequencies. The discreteness of quantum state is deduced and the ground-state wave function of avian genome is obtained. As the evolutionary inertia decreasing the classical phase of evolution is transformed into quantum phase. New species production is described by the quantum transition between discrete quantum states. The quantum transition rate is calculated which provides a clue to understand the law of the rapid post-Cretaceous radiation of neoavian birds. -
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. -
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. -
Bakalářská Práce
Univerzita Palackého v Olomouci Bakalářská práce Olomouc 2020 Klára Košatová Univerzita Palackého v Olomouci Přírodovědecká fakulta Katedra buněčné biologie a genetiky Cross-species amplifikace mikrosatelitů z řádu tučňáci a konzervovaných ptačích mikrosatelitů u čápa simbila (Ciconia abdimii) Bakalářská práce Klára Košatová Studijní program: Biologie Studijní obor: Molekulární a buněčná biologie Forma studia: Prezenční Olomouc 2020 Vedoucí práce: RNDr. Petr Nádvorník, Ph.D. Bibliografické údaje Jméno a příjmení autora: Klára Košatová Název práce: Cross-species amplifikace mikrosatelitů z řádu tučňáci a konzervovaných ptačích mikrosatelitů u čápa simbila (Ciconia abdimii) Typ práce: Bakalářská práce Pracoviště: Katedra buněčné biologie a genetiky, Přírodovědecká fakulta, Univerzita Palackého v Olomouci Vedoucí práce: RNDr. Petr Nádvorník, Ph.D. Rok obhajoby práce: 2020 Souhrn: V této bakalářské práci jsem se zabývala hledáním polymorfních mikrosatelitních lokusů u čápa simbila (Ciconia abdimii). V teoretické části jsem se věnovala vývoji a změnám taxonomického zařazení čápa simbila do systému ptáků, dále jsem popsala řád čápi (Ciconiiformes), do kterého je v současnosti řazena jediná čeleď čápovití (Ciconiidae). Popsala jsem mikrosatelity, jako molekulové markery a zaměřila jsem se na charakteristiku mikrosatelitů navržených pro řád tučňáci a univerzálních ptačích mikrosatelitů. V praktické části jsem provedla cross-species PCR amplifikaci celkem 173 mikrosatelitů na genomické DNA šesti nepříbuzných jedinců čápa simbila, s cílem nalezení -
Developmental Origins of Mosaic Evolution in the Avian Cranium
Developmental origins of mosaic evolution in the SEE COMMENTARY avian cranium Ryan N. Felicea,b,1 and Anjali Goswamia,b,c aDepartment of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; bDepartment of Life Sciences, The Natural History Museum, London SW7 5DB, United Kingdom; and cDepartment of Earth Sciences, University College London, London WC1E 6BT, United Kingdom Edited by Neil H. Shubin, The University of Chicago, Chicago, IL, and approved December 1, 2017 (received for review September 18, 2017) Mosaic evolution, which results from multiple influences shaping genes. For example, manipulating the expression of Fgf8 generates morphological traits and can lead to the presence of a mixture of correlated responses in the growth of the premaxilla and palatine ancestral and derived characteristics, has been frequently invoked in in archosaurs (11). Similarly, variation in avian beak shape and describing evolutionary patterns in birds. Mosaicism implies the size is regulated by two separate developmental modules (7). hierarchical organization of organismal traits into semiautonomous Despite the evidence for developmental modularity in the avian subsets, or modules, which reflect differential genetic and develop- skull, some studies have concluded that the cranium is highly in- mental origins. Here, we analyze mosaic evolution in the avian skull tegrated (i.e., not subdivided into semiautonomous modules) (9, using high-dimensional 3D surface morphometric data across a 10, 12). In light of recent evidence that diversity in beak mor- broad phylogenetic sample encompassing nearly all extant families. phology may not be shaped by dietary factors (12), it is especially We find that the avian cranium is highly modular, consisting of seven critical to investigate other factors that shape the evolution of independently evolving anatomical regions. -
Recurrent DCC Gene Losses During Bird Evolution
www.nature.com/scientificreports OPEN Recurrent DCC gene losses during bird evolution François Friocourt1, Anne-Gaelle Lafont2, Clémence Kress3, Bertrand Pain3, Marie Manceau4, Sylvie Dufour2 & Alain Chédotal1 Received: 27 June 2016 During development, midline crossing by axons brings into play highly conserved families of receptors Accepted: 31 October 2016 and ligands. The interaction between the secreted ligand Netrin-1 and its receptor Deleted in Colorectal Published: 27 February 2017 Carcinoma (DCC) is thought to control midline attraction of crossing axons. Here, we studied the evolution of this ligand/receptor couple in birds taking advantage of a wealth of newly sequenced genomes. From phylogeny and synteny analyses we can infer that the DCC gene has been conserved in most extant bird species, while two independent events have led to its loss in two avian groups, passeriformes and galliformes. These convergent accidental gene loss events are likely related to chromosome Z rearrangement. We show, using whole-mount immunostaining and 3Disco clearing, that in the nervous system of all birds that have a DCC gene, DCC protein expression pattern is similar to other vertebrates. Surprisingly, we show that the early developmental pattern of commissural tracts is comparable in all birds, whether or not they have a DCC receptor. Interestingly, only 4 of the 5 genes encoding secreted netrins, the DCC ligands in vertebrates, were found in birds, but Netrin-5 was absent. Together, these results support a remarkable plasticity of commissural axon guidance mechanisms in birds. Despite more than 600 million years of evolution, the basic components of the bilaterian brain wiring diagram are highly conserved1. -
Morphometric Analysis of the Gull Larus (Aves:Laridae) with Implications for Small Theropod Diversity in the Late Cretaceous
Morphometric analysis of the gull Larus (Aves:Laridae) with implications for small theropod diversity in the Late Cretaceous by Michel Haché A thesis submitted to the Faculty of Graduate and Postdoctoral Affairs in partial fulfillment of the requirements for the degree of Master of Science in Earth Science Carleton University Ottawa, Ontario © 2016, Michel Haché Abstract This project analyzed morphological diversity in the modern gull (Aves: Charadriiformes) genus Larus. Measurements of the post-cranial skeletons were made on specimens from six species of Larus and analyzed using Principal Component Analysis (PCA). Similar analyses were conducted on a series of theropod taxa. Landmark-based geometric morphometric analysis was also conducted on select skulls of gulls and analyzed using PCA. The results show that most of the gull species are very similar for the morphological parameters analyzed, only differing in overall body size, and, thus cannot be easily distinguished based on their skeletal morphology. These results were used as a modern analogue for inferring species diversity in the theropod fossil record. The implications of this study suggest that skeletal morphology, without the addition of soft tissue and behavior data available for modern birds, may not be able to distinguish closely related species of interbreeding, non-avian theropods in the fossil record. This suggests that the species diversity of extinct non-avian theropods was likely higher than can be of determined from their skeletal remains. 1 Acknowledgements I would like to thank my supervisors, Dr. Michael Ryan and Dr. Tim Patterson for their support over the past two years. I would like to thank Elizabeth Anderson for her patience and for helping me with writing this thesis.