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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
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. -
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. -
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. -
Icp Publications 2006-2021
ICP PUBLICATIONS 2006-2021 Last updated: 1 September 2021 In press and published online _______________________________________________________________________ SCI papers (indexed in JCR) 1. Abella, J., Martín-Perea, D. M., Valenciano, A., Hontecillas, D., Montoya, P., & Morales, J. (2021, published online). Coprolites in natural traps: direct evidence of bone eating carnivorans from the Late Miocene site of Batallones-3 (Madrid, Spain). Lethaia. https://doi.org/10.1111/let.12438 2. Agustí, J., Espresate, J., & Piñero, P. (2020, published in press). Dental variation in the endemic dormouse Hypnomys Bate 1918 and its implications for the palaeogeographic evolution of the Balearic Islands (Western Mediterranean) during the late Neogene-Quaternary. Historical Biology. https://doi.org/10.1080/08912963.2020.1852557 3. Alba, D. M., Robles, J. M., Valenciano, A., Abella, J., & Casanovas-Vilar, I. (2021, published online). A new species of Eomellivora from the latest Aragonian of Abocador de Can Mata (NE Iberian Peninsula). Historical Biology. https://doi.org/10.1080/08912963.2021.1943380 4. Arias-Martorell, J., Zeininger, A., & Kivell, T. L. (in press). Trabecular structure of the elbow reveals divergence in knuckle-walking biomechanical strategies of African apes. Evolution. 5. Bouchet, F., Urciuoli, A., Beaudet, A., Pina, M., Moyà-Solà, S., & Alba, D. M. (in press). Comparative anatomy of the carotid canal in the Miocene small-bodied catarrhine Pliobates cataloniae. Journal of Human Evolution. 6. Caballero, Ó., Montoya, P., Crespo, V. D., Morales, J., & Abella, J. (2020, published online). The autopodial skeleton of Paracamelus aguirrei (Morales 1984) (Tylopoda, Mammalia) from the late Miocene site of Venta del Moro (Valencia, Spain). Journal of Iberian Geology. -
Comptes Rendus Palevol Bite Force of the Extinct Pleistocene Cave Bear
C. R. Palevol 9 (2010) 31–37 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Contents lists available at ScienceDirect provided by RERO DOC Digital Library Comptes Rendus Palevol www.sciencedirect.com Systematic palaeontology (Vertebrate palaeontology) Bite force of the extinct Pleistocene Cave bear Ursus spelaeus Rosenmüller from Europe Force de la morsure de l’ours des cavernes Ursus spelaeus Rosenmüller du Pléistocène d’Europe Aurora Grandal-d’Anglade Instituto Universitario de Xeoloxía, Universidade da Coru˜na, Campus de Elvi˜na s/n, 15071 A Coru˜na, Spain article info abstract Article history: In this paper, I have made a theoretical calculation of the Cave bear’s bite force (BF) following Received 7 April 2009 the “dry skull method” and I present for the first time BF data that can be of interest to Accepted after revision 6 October 2009 elucidate the mechanisms underlying the dietary choice of the Cave bears. In the skulls Available online 22 December 2009 studied, males show higher BF than females in absolute terms, but more similar with regard to their body mass, which partly compensates for the smaller size of the females. The whole Presented by Philippe Taquet sample studied shows lower BF in the upper carnassial than those of large cats, similar to the one calculated for the Giant panda and higher than that of Polar bear. Keywords: © 2009 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved. Ursus spelaeus Bite force Sexual dimorphism Herbivore feeding résumé Mots clés : Dans ce travail, j’ai réalisé un calcul théorique de la force de morsure (BF) de l’ours des cav- Ursus spelaeus ernes, en suivant la « dry skull method », et j’y présente, pour la première fois, des données Force de morsure de BF sur cette espèce, qui peuvent être d’un grand intérêt pour comprendre les mécan- Dimorphisme sexuel ismes qui interviennent dans les préférences trophiques de l’ours des cavernes. -
Ailuropoda Melanoleuca)
Naturwissenschaften (2011) 98:107–116 DOI 10.1007/s00114-010-0748-x ORIGINAL PAPER Cranial shape transformation in the evolution of the giant panda (Ailuropoda melanoleuca) Borja Figueirido & Paul Palmqvist & Juan A. Pérez-Claros & Wei Dong Received: 17 August 2010 /Revised: 16 November 2010 /Accepted: 17 November 2010 /Published online: 4 December 2010 # Springer-Verlag 2010 Abstract In this study, landmark-based methods of Ailuropoda lineage, as previously thought, but underwent a geometric morphometrics are used for investigating the number of changes during more than 2 Myr. main aspects of cranial shape transformation in the evolution of the giant panda, Ailuropoda melanoleuca. Keywords Ailuropoda . Cranial morphology. Evolution . Specifically, we explore if the highly derived cranial Geometric morphometrics adaptations for bamboo feeding of the living panda were developed early in the panda's lineage. Results obtained show that the overall cranial morphologies of the oldest Introduction known panda, the “pygmy” Ailuropoda microta,andthe late Pleistocene Ailuropoda baconi are both very similar The evolutionary history of the giant panda, Ailuropoda to that of their closest living relative, A. melanoleuca, melanoleuca, has been debated for decades and is still a which agrees with a previous proposal based on qualita- matter of controversy today. The central core of the debate tive criteria. However, we also describe several differ- lies in the phylogenetic relationships of Ailuropoda,an ences between the crania of A. microta, A. baconi,andA. issue that is not clarified by the scarce fossil record melanoleuca, including the development of the postor- available for the panda lineage (Bininda-Emonds 2004; bital process, the orientation of the occipital region, and Hunt 2004; Jin et al. -
Paleodiversity of the Superfamily Ursoidea (Carnivora, Mammalia) in the Spanish Neogene, Related to Environmental Changes
Journal of Iberian Geology 40 (1) 2014: 11-18 http://dx.doi.org/10.5209/rev_JIGE.2014.v40.n1.44083 www.ucm.es /info/estratig/journal.htm ISSN (print): 1698-6180. ISSN (online): 1886-7995 Paleodiversity of the Superfamily Ursoidea (Carnivora, Mammalia) in the Spanish Neogene, related to environmental changes J. Abella1,2*, P. Montoya3, J. Morales2 1Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICP, Campus de la UAB s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain. 2Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain. 3Departament de Geologia, Àrea de Paleontologia, Universitat de València, Doctor Moliner 50, 46100 Burjassot, Spain. E-mail addresses: [email protected] (J.A., *corresponding author); [email protected] (P.M.); [email protected] (J.M.) Received: 25 May 2013 / Accepted: 3 December 2013 / Available online: 25 February 2014 Abstract In the present study we analyse the diversity of the Superfamily Ursoidea during the Neogene of the Iberian Peninsula to further compare it with that of the Neogene of Western Europe to find the different associations of this group. The results indicate that both the diversity and the taxonomy amongst these two regions show important variations, thus letting their interpretation in terms of climatic differentiation. We might relate variations in the abundance of the Ursoidea to the environmental fluctuations taking place during the Miocene and Pliocene. Therefore, they could enable us to reach the assessment of these biogeographical distributions in order to deduce the preferential niches of each different group of Ursoidea. Keywords: Carnivora, Hemicyonidae, Ursidae, Iberian Peninsula, Miocene, Pliocene Resumen En este trabajo se analiza la diversidad de la Superfamilia Ursoidea durante el Neógeno de la Península Ibérica, comparándola con la de Europa Occidental de la misma época, con el objetivo de localizar las diferentes asociaciones de los miembros de este grupo. -
Virtual Cranial Endocast of the Oldest Giant Panda (Ailuropoda Microta) Reveals Great Similarity to That of Its Extant Relative
Naturwissenschaften (2008) 95:1079–1083 DOI 10.1007/s00114-008-0419-3 SHORT COMMUNICATION Virtual cranial endocast of the oldest giant panda (Ailuropoda microta) reveals great similarity to that of its extant relative Wei Dong Received: 27 January 2008 /Revised: 3 June 2008 /Accepted: 4 June 2008 / Published online: 4 July 2008 # Springer-Verlag 2008 Abstract Recent development of computed tomography Keywords Giant panda . Paleoneurology. Evolution . and three-dimensional visualization techniques has enabled Computed tomography. Plio–Pleistocene the non-destructive inspection of the endocast morphology of fossil neurocranium, the basic material for paleoneuro- logical study. A virtual cranial endocast was reconstructed Introduction based on the first skull of the oldest giant panda, Ailuropoda microta, discovered recently and dated at more The rarity of natural fossil cranial endocasts as well as than 2 Myr (million years) ago. It was compared with that avoidance of destructive dissection on precious skulls often of the extant giant panda (A. melanoleuca) and that of the hinders paleoneurological research. With the development polar bear (Ursus maritimus), as well as CT slices of the of computed tomography (CT) and three-dimensional late Pleistocene A. baconi. The overall endocast morphology visualization techniques, it becomes more and more of A. microta is more similar to that of A. baconi and A. practical for paleontologists to carry out noninvasive melanoleuca than to that of U. maritimus. The absolute dissection on rare and precious fossil skulls to learn endocast size is the smallest in A. microta, largest in A. endocast morphology and undertake quantitative analyses baconi, and intermediate in A. melanoleuca.However,the (Zollikofer and Ponce de León 2000; Falk et al. -
A Survey of Cenozoic Mammal Baramins
The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 217-221 Article 43 2018 A Survey of Cenozoic Mammal Baramins C Thompson Core Academy of Science Todd Charles Wood Core Academy of Science Follow this and additional works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Thompson, C., and T.C. Wood. 2018. A survey of Cenozic mammal baramins. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 217–221. Pittsburgh, Pennsylvania: Creation Science Fellowship. Thompson, C., and T.C. Wood. 2018. A survey of Cenozoic mammal baramins. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 217–221, A1-A83 (appendix). Pittsburgh, Pennsylvania: Creation Science Fellowship. A SURVEY OF CENOZOIC MAMMAL BARAMINS C. Thompson, Core Academy of Science, P.O. Box 1076, Dayton, TN 37321, [email protected] Todd Charles Wood, Core Academy of Science, P.O. Box 1076, Dayton, TN 37321, [email protected] ABSTRACT To expand the sample of statistical baraminology studies, we identified 80 datasets sampled from 29 mammalian orders, from which we performed 82 separate analyses.