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An R Package for Visualizing Bayesian Phylogenetic Analyses from Revbayes
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.10.443470; this version posted May 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes Carrie M. Tribble1, 2, 3, ∗, William A. Freyman4, Michael J. Landis5, Jun Ying Lim6, Joelle¨ Barido-Sottani7, Bjørn Tore Kopperud8, 9, Sebastian Hohna¨ 8, 9, and Michael R. May1, 2 1Department of Integrative Biology University of California, Berkeley, CA 94709, USA 2University Herbarium, University of California, Berkeley, CA 94709, USA 3Current address: School of Life Sciences, University of Hawai‘i at M¯anoa,Honolulu, HI, 96822, USA 423andMe, Inc., Sunnyvale, CA, 94086, USA 5Department of Biology, Washington University in St. Louis, MO 63130, USA 6School of Biological Sciences, Nanyang Technological University, Singapore 639798 7Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA 8GeoBio-Center, Ludwig-Maximilians-Universit¨atM¨unchen,80333 Munich, Germany 9Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universit¨atM¨unchen,80333 Munich, Germany ∗E-mail: [email protected] Summary 1. Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological stud- ies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, and communicating their key results. 2. We present RevGadgets, an R package for creating publication-quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages). -
Protarctos Abstrusus
www.nature.com/scientificreports OPEN A basal ursine bear (Protarctos abstrusus) from the Pliocene High Arctic reveals Eurasian afnities Received: 18 August 2017 Accepted: 24 November 2017 and a diet rich in fermentable Published: xx xx xxxx sugars Xiaoming Wang 1,2,3, Natalia Rybczynski4,5, C. Richard Harington4, Stuart C. White6 & Richard H. Tedford3 The skeletal remains of a small bear (Protarctos abstrusus) were collected at the Beaver Pond fossil site in the High Arctic (Ellesmere I., Nunavut). This mid-Pliocene deposit has also yielded 12 other mammals and the remains of a boreal-forest community. Phylogenetic analysis reveals this bear to be basal to modern bears. It appears to represent an immigration event from Asia, leaving no living North American descendants. The dentition shows only modest specialization for herbivory, consistent with its basal position within Ursinae. However, the appearance of dental caries suggest a diet high in fermentable- carbohydrates. Fossil plants remains, including diverse berries, suggests that, like modern northern black bears, P. abstrusus may have exploited a high-sugar diet in the fall to promote fat accumulation and facilitate hibernation. A tendency toward a sugar-rich diet appears to have arisen early in Ursinae, and may have played a role in allowing ursine lineages to occupy cold habitats. In 1970, Philip Bjork described a small fossil bear from the Pliocene Glenn’s Ferry Formation of southwestern Idaho. Based on a single m1 as the holotype, he was understandably perplexed and named it Ursus abstrusus. Additional material has not been forthcoming since its initial description and this bear has remained an enigma. -
Origin of an Assemblage Massively Dominated by Carnivorans from the Miocene of Spain
Origin of an Assemblage Massively Dominated by Carnivorans from the Miocene of Spain M. Soledad Domingo1*, M. Teresa Alberdi2, Beatriz Azanza3, Pablo G. Silva4, Jorge Morales2 1 Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, United States of America, 2 Departamento de Paleobiologı´a, Museo Nacional de Ciencias Naturales-Consejo Superior de Investigaciones Cientı´ficas, Madrid, Spain, 3 Departamento de Ciencias de la Tierra, Facultad Ciencias, Instituto Universitario de Investigacio´n en Ciencias Ambientales de Arago´n, Universidad de Zaragoza, Zaragoza, Spain, 4 Departamento de Geologı´a, Universidad de Salamanca, Escuela Polite´cnica Superior de A´ vila, A´ vila, Spain Abstract Carnivoran-dominated fossil sites provide precious insights into the diversity and ecology of species rarely recovered in the fossil record. The lower level assemblage of Batallones-1 fossil site (Late Miocene; Madrid Basin, Spain) has yielded one of the most abundant and diversified carnivoran assemblage ever known from the Cenozoic record of mammals. A comprehensive taphonomic study is carried out here in order to constrain the concentration mode of this remarkable assemblage. Another distinctive feature of Batallones-1 is that the accumulation of carnivoran remains took place in the context of a geomorphological landform (cavity formation through a piping process) practically unknown in the generation of fossil sites. Two characteristics of the assemblage highly restrict the probable causes for the accumulation of the remains: (1) the overwhelming number of carnivorans individuals; and (2) the mortality profiles estimated for the four most abundant taxa do not correspond to the classic mortality types but rather were the consequence of the behavior of the taxa. -
Chapter 1 - Introduction
EURASIAN MIDDLE AND LATE MIOCENE HOMINOID PALEOBIOGEOGRAPHY AND THE GEOGRAPHIC ORIGINS OF THE HOMININAE by Mariam C. Nargolwalla A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Anthropology University of Toronto © Copyright by M. Nargolwalla (2009) Eurasian Middle and Late Miocene Hominoid Paleobiogeography and the Geographic Origins of the Homininae Mariam C. Nargolwalla Doctor of Philosophy Department of Anthropology University of Toronto 2009 Abstract The origin and diversification of great apes and humans is among the most researched and debated series of events in the evolutionary history of the Primates. A fundamental part of understanding these events involves reconstructing paleoenvironmental and paleogeographic patterns in the Eurasian Miocene; a time period and geographic expanse rich in evidence of lineage origins and dispersals of numerous mammalian lineages, including apes. Traditionally, the geographic origin of the African ape and human lineage is considered to have occurred in Africa, however, an alternative hypothesis favouring a Eurasian origin has been proposed. This hypothesis suggests that that after an initial dispersal from Africa to Eurasia at ~17Ma and subsequent radiation from Spain to China, fossil apes disperse back to Africa at least once and found the African ape and human lineage in the late Miocene. The purpose of this study is to test the Eurasian origin hypothesis through the analysis of spatial and temporal patterns of distribution, in situ evolution, interprovincial and intercontinental dispersals of Eurasian terrestrial mammals in response to environmental factors. Using the NOW and Paleobiology databases, together with data collected through survey and excavation of middle and late Miocene vertebrate localities in Hungary and Romania, taphonomic bias and sampling completeness of Eurasian faunas are assessed. -
On the Socio-Sexual Behaviour of the Extinct Ursid Indarctos Arctoides: an Approach Based on Its Baculum Size and Morphology
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC On the Socio-Sexual Behaviour of the Extinct Ursid Indarctos arctoides: An Approach Based on Its Baculum Size and Morphology Juan Abella1,2*, Alberto Valenciano3,4, Alejandro Pe´rez-Ramos5, Plinio Montoya6, Jorge Morales2 1 Institut Catala` de Paleontologia Miquel Crusafont, Universitat Auto`noma de Barcelona. Edifici ICP, Campus de la UAB s/n, Barcelona, Spain, 2 Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain, 3 Departamento de Geologı´a Sedimentaria y Cambio Medioambiental. Instituto de Geociencias (CSIC, UCM), Madrid, Spain, 4 Departamento de Paleontologı´a, Facultad de Ciencias Geolo´gicas UCM, Madrid, Spain, 5 Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Vale`ncia, Paterna, Spain, 6 Departament de Geologia, A` rea de Paleontologia, Universitat de Vale`ncia, Burjassot, Spain Abstract The fossil bacula, or os penis, constitutes a rare subject of study due to its scarcity in the fossil record. In the present paper we describe five bacula attributed to the bear Indarctos arctoides Depe´ret, 1895 from the Batallones-3 site (Madrid Basin, Spain). Both the length and morphology of this fossil bacula enabled us to make interpretative approaches to a series of ecological and ethological characters of this bear. Thus, we suggest that I. arctoides could have had prolonged periods of intromission and/or maintenance of intromission during the post-ejaculatory intervals, a multi-male mating system and large home range sizes and/or lower population density. Its size might also have helped females to choose from among the available males. -
DUIM VAN DE PANDA Gratis Epub, Ebook
DUIM VAN DE PANDA GRATIS Auteur: Stephen Jay Gould Aantal pagina's: 303 pagina's Verschijningsdatum: none Uitgever: none EAN: 9789025400255 Taal: nl Link: Download hier Paleontoloog-superster overleden Je reageert onder je Twitter account. Je reageert onder je Facebook account. Houd me via e-mail op de hoogte van nieuwe reacties. Houd me via e-mail op de hoogte van nieuwe berichten. Spring naar inhoud. De extra duim van de panda Posted on januari 30, by kaspar55 — Plaats een reactie. Share this: Twitter Facebook. Vind ik leuk: Like Laden Geplaatst in De Pandabeer , Panda artikel , Panda informatie. Geef een reactie Reactie annuleren Vul je reactie hier in Vul je gegevens in of klik op een icoon om in te loggen. Uw vraag. Verstuur mijn vraag. Alle boeken zijn compleet en verkeren in normale antiquarische staat, tenzij anders beschreven. Kleine onvolkomenheden, zoals een ingeplakte ex- libris of een naam op het schutblad, zijn niet altijd vermeld U handelt deze order direct af met In libris libertas Na uw bestelling ontvangen u en In libris libertas een bevestiging per e-mail. In de e-mail staan de naam, adres, woonplaats en telefoonnummer van In libris libertas vermeld De Koper betaalt de verzendkosten, tenzij anders overeen gekomen In libris libertas kan betaling vooraf vragen Boekwinkeltjes. Als u een geschil hebt met één of meer gebruikers, dient u dit zelf op te lossen. U vrijwaart Boekwinkeltjes. Onthoud mijn gegevens. Uit onderz De ondernemingsrechtbank verwerpt het reddingsplan voor de plantagegroep van Hein Deprez. Hij staa Lees de volledige krant digitaal. Mijn DS Mijn account Afmelden. -
Kretzoiarctos Gen. Nov., the Oldest Member of the Giant Panda Clade
Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade Juan Abella1*, David M. Alba2, Josep M. Robles2,3, Alberto Valenciano4,5, Cheyenn Rotgers2,3, Rau¨ l Carmona2,3, Plinio Montoya6, Jorge Morales1 1 Museo Nacional de Ciencias Naturales-Centro superior de Investigaciones Cientı´ficas (MNCN-CSIC), Madrid, Spain, 2 Institut Catala` de Paleontologia Miquel Crusafont, Cerdanyola del Valle`s, Barcelona, Spain, 3 FOSSILIA Serveis Paleontolo`gics i Geolo`gics, S.L., Sant Celoni, Barcelona, Spain, 4 Departamento de Geologı´a Sedimentaria y Cambio Clima´tico, Instituto de Geociencias; UCM-CSIC (Universidad Complutense de Madrid-Centro Superior de Investigaciones Cientı´ficas), Madrid, Spain, 5 Departamento de Paleontologı´a, Facultad de Ciencias Geolo´gicas UCM (Universidad Complutense de Madrid), Madrid, Spain, 6 Departament de Geologia, A` rea de Paleontologia, Universitat de Vale`ncia, Burjassot, Valencia, Spain Abstract The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. -
Master Universitario En Paleobiología Y Registro Fósil / Paleobiology and Fossil Record
MASTER UNIVERSITARIO EN PALEOBIOLOGÍA Y REGISTRO FÓSIL / PALEOBIOLOGY AND FOSSIL RECORD UNIVERSITAT AUTÒNOMA DE BARCELONA UNIVERSITAT DE BARCELONA Febrer 2018 1 1. DESCRIPCIÓN DEL TÍTULO 1.1 Denominación Denominación del título: Paleobiología y registro fósil/ Paleobiology and fossil record Especialidades: sin especialidades Créditos totales: 60 Rama de adscripción: Ciencias ISCED 1: Geología y Meteorología ISCED 2: Biología y Bioquímica 1.2 Universidad y centro solicitante: Universidad: Universitat Autònoma de Barcelona Centro: Facultad de Ciencias Universidad: Universidad de Barcelona Centro: Facultad de Ciencias de la Tierra Institut Català de Paleontologia. 1.3 Número de plazas de nuevo ingreso y tipo de enseñanza: Número de plazas de nuevo ingreso 2017/2018: 25 Número de plazas de nuevo ingreso 2018/2019: 25 Tipo de enseñanza: Presencial 1.4 Criterios y requisitos de matriculación Número mínimo y máximo de créditos de matrícula: Máster de 60 Tiempo completo Tiempo parcial créditos Mat.mínima Mat.máxima Mat.mínima Mat.máxima 1r curso 60 60 30 42 Resto de cursos 0 0 30 42 Normativa de permanencia 1.5 Resto de información necesaria para la expedición del Suplemento Europeo del Título No corresponde Profesiones a las que capacita No corresponde Lenguas utilizadas en el proceso formativo Inglés (85%), castellano (15%). 2 2. JUSTIFICACIÓN 2.1 Justificación del título propuesto, argumentando el interés académico, científico y profesional del mismo Este máster tiene sus antecedentes, en cuanto a temática y parte del profesorado, en el antiguo ‘Master en Paleontología’ que estaba muy dirigido a estudios sistemáticos y taxonómicos de los grupos tanto de plantas como de animales fósiles. La nueva propuesta incorpora conceptos que han tenido un gran desarrollo reciente en el campo de la biología (modelización ecológica, morfometría geométrica, paleofisiología, paleogenética, paleodemografía etc.) para proporcionar un enfoque más paleobiológico al registro fósil. -
ABSTRACT How Sabertoothed Felids Have Evolved Their Iconic Morphology Remains Unclear Because of the Patchy Fossil Record of Early Machairodontines
Journal of Mammalian Evolution https://doi.org/10.1007/s10914-021-09541-0 Accepted: 8 March 2021 Morphometric analysis of the mandible of primitive sabertoothed felids from the late Miocene of Spain Short title: Morphometric analysis of early sabertoothed felids Narimane Chatar1,*, Valentin Fischer1, Gema Siliceo2, Mauricio Antón2, Jorge Morales2, and Manuel J. Salesa2 1 Evolution and Diversity Dynamics Lab, Université de Liège, Belgium 2 Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal, 2. 28006 Madrid, Spain * Corresponding author: [email protected] ABSTRACT How sabertoothed felids have evolved their iconic morphology remains unclear because of the patchy fossil record of early machairodontines. Batallones localities in the Madrid region (Spain) have the potential to clarify this as two sites have yielded hundreds of fossils of the early machairodontines Promegantereon ogygia and Machairodus aphanistus. Previous analyses suggested that these two sites are not contemporaneous and a morphological drift between cavities was described for these two species; characterizing intraspecific variability is thus important to better understand the evolution of machairodontines. To tackle this issue, we modelled 62 felid mandibles in 3D using a laser scanner. We applied 3D geometric morphometrics (3D GM) and linear morphometrics on these models to test for differences in populations and to better characterize the morphology of early machairodontines. Both linear measurements and 3D data reveal an absence of morphological changes in mandible shape between the two sites. Batallones machairodontines are closer to felines than to other, more derived machairodontines in mandibular morphology, suggesting the existence of rapid shift in the mandibular shape between primitive and derived members of the clade. -
A Late Miocene Ursavus Skull from Guanghe, Gansu, China
-302 第52卷 第3期 古 脊 椎 动 物 学 报 pp. 265 2014年7月 VERTEBRATA PALASIATICA figs. 1-9 A Late Miocene Ursavus skull from Guanghe, Gansu, China QIU Zhan-Xiang DENG Tao WANG Ban-Yue (Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences Beijing 100044 [email protected]) Abstract An almost complete Ursavus skull in association with its mandible is described. The skull was recently found from upper part of Liushu Formation in Linxia Basin. Its stratigraphic level and geologic age are correlated to the late Bahean ALMA/S, ~8 Ma. It represents a new species, here named Ursavus tedfordi. Cladistic analysis is conducted using the TNT software, based on a matrix of 11 taxa and 37 characters. The tree 5 of the 8 most parsimonious trees is chosen as the most reliable to reflect the phylogenetic history of the ursid clade. As the tree 5 shows, after divergence from the Oligocene-Early Miocene hemicyonids (Cephalogale), the ursid clade first yielded two stem-taxa: Ballusia elmensis and B. orientalis, the latter of which being an aberrant branch. Then, two major subclades emerged: one comprising Kretzoiarctos, Agriarctos and Ailurarctos, the other containing all Ursavus species and their descendants including all living bears (excluding Ailuropoda). Kretzoiarctos may not be the direct ancestral form of the giant panda as Abella and colleagues (2012) suggested, but the ancestral form of the lineage of Indarctos (+Agriotherium ?). Among the numerous Ursavus species, U. tedfordi is the most advanced and closest related to the living bears (excluding Ailuropoda) in morphology, however, might belong to a side-branch, judging by the autapomorphies possessed by it. -
Download Full Article in PDF Format
New stem giraffoid ruminants from the early and middle Miocene of Namibia Jorge MORALES Departamento de Paleobiologia, Museo Nacional de Ciencias Naturales, CSIC, José Gutierrez Abascal 2, E-28006, Madrid (Spain) Dolores SORIA Departamento de Paleobiologia, Museo Nacional de Ciencias Naturales, CSIC, José Gutierrez Abascal 2, E-28006, Madrid (Spain) Martin PICKFORD Chaire de Paléoanthropologie et de Préhistoire, Collège de France, 11 place Marcelin-Berthelot, F-75005, Paris (France) Laboratoire de Paléontologie, UMR 8569 du CNRS, Muséum national d'Histoire naturelle 8 rue de Button, F-75231 Paris cedex 05 (France) Morales J., Soria D. & Pickford M. 1999. — New stem giraffoid ruminants from the early and middle Miocene of Namibia. Geodiversitas (21)2: 229-253. ABSTRACT At the early and middle Miocene localities of the Sperrgebiet, Namibia, new material of climacoceratid tuminants have been collected recently. From Elisabethfeld we describe new material belonging to Propalaeoryx austroafri- canus Stromer, 1926, together with a new genus and species of climacocera tid Sperrgebietomeryx wardi n. gen., n. sp., a species without frontal appendages close to Propalaeoryx and to primitive early Miocene European ruminants such as Andegameryx. From the locality of Arrisdrift, we define another new genus and species of climacoceratid with frontal appendages, KEYWORDS Ruminantia, Orangemeryx bendey n. gen., n. sp., characterized by its complex tined frontal Giraffoidea, apophyses. Comparison of the dentition and postcranial skeleton of this Climacoceratidae, genus and those of Sperrgebietomeryx suggests a close phylogenetic relation Miocene, Namibia. ships between them. 1999 • 21 (2) 229 Morales J., Soria D. & Pickford M. RESUME Nouveaux ruminants giraffoïdes du Miocène ancien et moyen de Namibie. -
Early Miocene Ruminants of Wallenried (USM, Aquitanian/Switzerlan) : Sedimentology, Biostratigraphy and Paleoecology
Early Miocene ruminants of Wallenried (USM, Aquitanian/Switzerlan) : sedimentology, biostratigraphy and paleoecology Autor(en): Becker, Damien / Rössner, Gertrud E. / Picot, Laurent Objekttyp: Article Zeitschrift: Eclogae Geologicae Helvetiae Band (Jahr): 94 (2001) Heft 3 PDF erstellt am: 11.10.2021 Persistenter Link: http://doi.org/10.5169/seals-168911 Nutzungsbedingungen Die ETH-Bibliothek ist Anbieterin der digitalisierten Zeitschriften. Sie besitzt keine Urheberrechte an den Inhalten der Zeitschriften. Die Rechte liegen in der Regel bei den Herausgebern. Die auf der Plattform e-periodica veröffentlichten Dokumente stehen für nicht-kommerzielle Zwecke in Lehre und Forschung sowie für die private Nutzung frei zur Verfügung. Einzelne Dateien oder Ausdrucke aus diesem Angebot können zusammen mit diesen Nutzungsbedingungen und den korrekten Herkunftsbezeichnungen weitergegeben werden. Das Veröffentlichen von Bildern in Print- und Online-Publikationen ist nur mit vorheriger Genehmigung der Rechteinhaber erlaubt. Die systematische Speicherung von Teilen des elektronischen Angebots auf anderen Servern bedarf ebenfalls des schriftlichen Einverständnisses der Rechteinhaber. Haftungsausschluss Alle Angaben erfolgen ohne Gewähr für Vollständigkeit oder Richtigkeit. Es wird keine Haftung übernommen für Schäden durch die Verwendung von Informationen aus diesem Online-Angebot oder durch das Fehlen von Informationen. Dies gilt auch für Inhalte Dritter, die über dieses Angebot zugänglich sind. Ein Dienst der ETH-Bibliothek ETH Zürich, Rämistrasse 101, 8092 Zürich, Schweiz, www.library.ethz.ch http://www.e-periodica.ch 0012-9402/01/030547-18 $1.50 + 0.20/0 Eclogae geol. Helv. 94 (2001 547-564 Birkhäuser Verlag. Basel. 2001 Early Miocene ruminants of Wallenried (USM, Aquitanian / Switzerland): Sedimentology, biostratigraphy and paleoecology Damien Becker1. Gertrud E. Rössner2, Laurent Picot1 & Jean-Pierre Berger1 Key words: USM.