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A Phylogenomic Analysis of Turtles ⇑ Nicholas G
Molecular Phylogenetics and Evolution 83 (2015) 250–257 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A phylogenomic analysis of turtles ⇑ Nicholas G. Crawford a,b,1, James F. Parham c, ,1, Anna B. Sellas a, Brant C. Faircloth d, Travis C. Glenn e, Theodore J. Papenfuss f, James B. Henderson a, Madison H. Hansen a,g, W. Brian Simison a a Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA b Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA c John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA d Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA e Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA f Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA g Mathematical and Computational Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 9171, USA article info abstract Article history: Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and Received 11 July 2014 prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle Revised 16 October 2014 phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of Accepted 28 October 2014 aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and Available online 4 November 2014 an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. -
Phylogenetic Comparative Methods: a User's Guide for Paleontologists
Phylogenetic Comparative Methods: A User’s Guide for Paleontologists Laura C. Soul - Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA David F. Wright - Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA and Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA Abstract. Recent advances in statistical approaches called Phylogenetic Comparative Methods (PCMs) have provided paleontologists with a powerful set of analytical tools for investigating evolutionary tempo and mode in fossil lineages. However, attempts to integrate PCMs with fossil data often present workers with practical challenges or unfamiliar literature. In this paper, we present guides to the theory behind, and application of, PCMs with fossil taxa. Based on an empirical dataset of Paleozoic crinoids, we present example analyses to illustrate common applications of PCMs to fossil data, including investigating patterns of correlated trait evolution, and macroevolutionary models of morphological change. We emphasize the importance of accounting for sources of uncertainty, and discuss how to evaluate model fit and adequacy. Finally, we discuss several promising methods for modelling heterogenous evolutionary dynamics with fossil phylogenies. Integrating phylogeny-based approaches with the fossil record provides a rigorous, quantitative perspective to understanding key patterns in the history of life. 1. Introduction A fundamental prediction of biological evolution is that a species will most commonly share many characteristics with lineages from which it has recently diverged, and fewer characteristics with lineages from which it diverged further in the past. This principle, which results from descent with modification, is one of the most basic in biology (Darwin 1859). -
1 Integrative Biology 200 "PRINCIPLES OF
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler March 14, 2018. Classification II: Phylogenetic taxonomy including incorporation of fossils; PhyloCode I. Phylogenetic Taxonomy - the argument for rank-free classification A number of recent calls have been made for the reformation of the Linnaean hierarchy (e.g., De Queiroz & Gauthier, 1992). These authors have emphasized that the existing system is based in a non-evolutionary world-view; the roots of the Linnaean hierarchy are in a specially- created world-view. Perhaps the idea of fixed, comparable ranks made some sense under that view, but under an evolutionary world view they don't make sense. There are several problems with the current nomenclatorial system: 1. The current system, with its single type for a name, cannot be used to precisely name a clade. E.g., you may name a family based on a certain type specimen, and even if you were clear about what node you meant to name in your original publication, the exact phylogenetic application of your name would not be clear subsequently, after new clades are added. 2. There are not nearly enough ranks to name the thousands of levels of monophyletic groups in the tree of life. Therefore people are increasingly using informal rank-free names for higher- level nodes, but without any clear, formal specification of what clade is meant. 3. Most aspects of the current code, including priority, revolve around the ranks, which leads to instability of usage. For example, when a change in relationships is discovered, several names often need to be changed to adjust, including those of groups whose circumscription has not changed. -
Crown Clades in Vertebrate Nomenclature
2008 POINTS OF VIEW 173 Wiens, J. J. 2001. Character analysis in morphological phylogenetics: Wilkins, A. S. 2002. The evolution of developmental pathways. Sinauer Problems and solutions. Syst. Biol. 50:689–699. Associates, Sunderland, Massachusetts. Wiens, J. J., and R. E. Etheridge. 2003. Phylogenetic relationships of Wright, S. 1934a. An analysis of variability in the number of digits in hoplocercid lizards: Coding and combining meristic, morphometric, an inbred strain of guinea pigs. Genetics 19:506–536. and polymorphic data using step matrices. Herpetologica 59:375– Wright, S. 1934b. The results of crosses between inbred strains 398. of guinea pigs differing in number of digits. Genetics 19:537– Wiens, J. J., and M. R. Servedio. 1997. Accuracy of phylogenetic analysis 551. including and excluding polymorphic characters. Syst. Biol. 46:332– 345. Wiens, J. J., and M. R. Servedio. 1998. Phylogenetic analysis and in- First submitted 28 June 2007; reviews returned 10 September 2007; traspecific variation: Performance of parsimony, likelihood, and dis- final acceptance 18 October 2007 tance methods. Syst. Biol. 47:228–253. Associate Editor: Norman MacLeod Syst. Biol. 57(1):173–181, 2008 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150801910469 Crown Clades in Vertebrate Nomenclature: Correcting the Definition of Crocodylia JEREMY E. MARTIN1 AND MICHAEL J. BENTON2 1UniversiteL´ yon 1, UMR 5125 PEPS CNRS, 2, rue Dubois 69622 Villeurbanne, France; E-mail: [email protected] 2Department of Earth Sciences, University of Bristol, Bristol, BS9 1RJ, UK; E-mail: [email protected] Downloaded By: [Martin, Jeremy E.] At: 19:32 25 February 2008 Acrown group is defined as the most recent common Dyke, 2002; Forey, 2002; Monsch, 2005; Rieppel, 2006) ancestor of at least two extant groups and all its descen- but rather expresses dissatisfaction with the increasingly dants (Gauthier, 1986). -
Phylocode: a Phylogenetic Code of Biological Nomenclature
PhyloCode: A Phylogenetic Code of Biological Nomenclature Philip D. Cantino and Kevin de Queiroz (equal contributors; names listed alphabetically) Advisory Group: William S. Alverson, David A. Baum, Harold N. Bryant, David C. Cannatella, Peter R. Crane, Michael J. Donoghue, Torsten Eriksson*, Jacques Gauthier, Kenneth Halanych, David S. Hibbett, David M. Hillis, Kathleen A. Kron, Michael S. Y. Lee, Alessandro Minelli, Richard G. Olmstead, Fredrik Pleijel*, J. Mark Porter, Heidi E. Robeck, Greg W. Rouse, Timothy Rowe*, Christoffer Schander, Per Sundberg, Mikael Thollesson, and Andre R. Wyss. *Chaired a committee that authored a portion of the current draft. Most recent revision: April 8, 2000 1 Table of Contents Preface Preamble Division I. Principles Division II. Rules Chapter I. Taxa Article 1. The Nature of Taxa Article 2. Clades Article 3. Hierarchy and Rank Chapter II. Publication Article 4. Publication Requirements Article 5. Publication Date Chapter III. Names Section 1. Status Article 6 Section 2. Establishment Article 7. General Requirements Article 8. Registration Chapter IV. Clade Names Article 9. General Requirements for Establishment of Clade Names Article 10. Selection of Clade Names for Establishment Article 11. Specifiers and Qualifying Clauses Chapter V. Selection of Accepted Names Article 12. Precedence Article 13. Homonymy Article 14. Synonymy Article 15. Conservation Chapter VI. Provisions for Hybrids Article 16. Chapter VII. Orthography Article 17. Orthographic Requirements for Establishment Article 18. Subsequent Use and Correction of Established Names Chapter VIII. Authorship of Names Article 19. Chapter IX. Citation of Authors and Registration Numbers Article 20. Chapter X. Governance Article 21. Glossary Table 1. Equivalence of Nomenclatural Terms Appendix A. -
Reconsidering Relationships Among Stem and Crown Group Pinaceae: Oldest Record of the Genus Pinus from the Early Cretaceous of Yorkshire, United Kingdom
Int. J. Plant Sci. 173(8):917–932. 2012. Ó 2012 by The University of Chicago. All rights reserved. 1058-5893/2012/17308-0006$15.00 DOI: 10.1086/667228 RECONSIDERING RELATIONSHIPS AMONG STEM AND CROWN GROUP PINACEAE: OLDEST RECORD OF THE GENUS PINUS FROM THE EARLY CRETACEOUS OF YORKSHIRE, UNITED KINGDOM Patricia E. Ryberg,* Gar W. Rothwell,1,y,z Ruth A. Stockey,y,§ Jason Hilton,k Gene Mapes,z and James B. Riding# *Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, U.S.A.; yDepartment of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331, U.S.A.; zDepartment of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701, U.S.A.; §Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E9, Canada; kSchool of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; and #British Geological Survey, Kingsley Dunham Centre, Keyworth, Nottingham NG12 5GG, United Kingdom This study describes a specimen that extends the oldest fossil evidence of Pinus L. to the Early Cretaceous Wealden Formation of Yorkshire, UK (131–129 million years ago), and prompts a critical reevaluation of criteria that are employed to identify crown group genera of Pinaceae from anatomically preserved seed cones. The specimen, described as Pinus yorkshirensis sp. nov., is conical, 5 cm long, and 3.1 cm in maximum diameter. Bract/scale complexes are helically arranged and spreading. Vasculature of the axis forms a complete cylinder with few resin canals in the wood, and the inner cortex is dominated by large resin canals. -
Genomic Data Do Not Support Comb Jellies As the Sister Group to All Other Animals
Genomic data do not support comb jellies as the sister group to all other animals Davide Pisania,b,1, Walker Pettc, Martin Dohrmannd, Roberto Feudae, Omar Rota-Stabellif, Hervé Philippeg,h, Nicolas Lartillotc, and Gert Wörheided,i,1 aSchool of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; bSchool of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; cLaboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France; dDepartment of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany; eDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; fDepartment of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige 38010, Italy; gCentre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d’Ecologie Expérimentale du CNRS, Moulis 09200, France; hDépartement de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7; and iBayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany Edited by Neil H. Shubin, The University of Chicago, Chicago, IL, and approved November 2, 2015 (received for review September 11, 2015) Understanding how complex traits, such as epithelia, nervous animal phylogeny separated ctenophores from all other ani- systems, muscles, or guts, originated depends on a well-supported mals (the “Ctenophora-sister” -
A North American Stem Turaco, and the Complex Biogeographic History of Modern Birds Daniel J
Field and Hsiang BMC Evolutionary Biology (2018) 18:102 https://doi.org/10.1186/s12862-018-1212-3 RESEARCHARTICLE Open Access A North American stem turaco, and the complex biogeographic history of modern birds Daniel J. Field1,2* and Allison Y. Hsiang2,3 Abstract Background: Earth’s lower latitudes boast the majority of extant avian species-level and higher-order diversity, with many deeply diverging clades restricted to vestiges of Gondwana. However, palaeontological analyses reveal that many avian crown clades with restricted extant distributions had stem group relatives in very different parts of the world. Results: Our phylogenetic analyses support the enigmatic fossil bird Foro panarium Olson 1992 from the early Eocene (Wasatchian) of Wyoming as a stem turaco (Neornithes: Pan-Musophagidae), a clade that is presently endemic to sub-Saharan Africa. Our analyses offer the first well-supported evidence for a stem musophagid (and therefore a useful fossil calibration for avian molecular divergence analyses), and reveal surprising new information on the early morphology and biogeography of this clade. Total-clade Musophagidae is identified as a potential participant in dispersal via the recently proposed ‘North American Gateway’ during the Palaeogene, and new biogeographic analyses illustrate the importance of the fossil record in revealing the complex historical biogeography of crown birds across geological timescales. Conclusions: In the Palaeogene, total-clade Musophagidae was distributed well outside the range of crown Musophagidae in the present day. This observation is consistent with similar biogeographic observations for numerous other modern bird clades, illustrating shortcomings of historical biogeographic analyses that do not incorporate information from the avian fossil record. -
Water Lilies As Emerging Models for Darwin's Abominable Mystery
OPEN Citation: Horticulture Research (2017) 4, 17051; doi:10.1038/hortres.2017.51 www.nature.com/hortres REVIEW ARTICLE Water lilies as emerging models for Darwin’s abominable mystery Fei Chen1, Xing Liu1, Cuiwei Yu2, Yuchu Chen2, Haibao Tang1 and Liangsheng Zhang1 Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants. The birth and rapid radiation of flowering plants has interested many scientists and was considered ‘an abominable mystery’ by Charles Darwin. In searching for the angiosperm evolutionary origin and its underlying mechanisms, the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages; however, little is known regarding the genetics and genomics of another basal angiosperm lineage, namely, the water lily. In this study, we reviewed current molecular research and note that water lily research has entered the genomic era. We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin’s ‘abominable mystery’. Four pantropical water lilies, especially the recently sequenced Nymphaea colorata, have characteristics such as small size, rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms. The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies. Horticulture Research (2017) 4, 17051; doi:10.1038/hortres.2017.51; Published online 4 October 2017 INTRODUCTION Ondinea, and Victoria.4,5 Floral organs differ greatly among each Ornamentals, cultural symbols and economic value family in the order Nymphaeales. -
Testing Hypotheses About the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set Ning Wang,1,2 Edward L
Testing Hypotheses about the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set Ning Wang,1,2 Edward L. Braun,1 and Rebecca T. Kimball*,1 1Department of Biology, University of Florida 2MOE Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China *Corresponding author: E-mail: rkimball@ufl.edu. Associate editor: Herve´ Philippe Abstract Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection Research article and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such relationship in need of independent evaluation is the position of Passeriformes (perching birds) in avian phylogeny. This order comprises more than half of all extant birds, and it includes one of the most important avian model systems (the zebra finch). Recent large-scale studies using morphology, Downloaded from mitochondrial, and nuclear sequence data have generated very different hypotheses about the sister group of Passeriformes, and all conflict with an older hypothesis generated using DNA–DNA hybridization. We used novel data from 30 nuclear loci, primarily introns, for 28 taxa to evaluate five major a priori hypotheses regarding the phylogenetic position of Passeriformes. Although previous studies have suggested that nuclear introns are ideal for the resolution of ancient avian relationships, introns have also been criticized because of the potential for alignment ambiguities and the loss of signal due to saturation. To http://mbe.oxfordjournals.org/ examine these issues, we generated multiple alignments using several alignment programs, varying alignment parameters, and using guide trees that reflected the different a priori hypotheses. -
Quarantine Host Range and Natural History of Gadirtha Fusca, a Potential Biological Control Agent of Chinese Tallowtree (Triadica Sebifera) in North America
DOI: 10.1111/eea.12737 Quarantine host range and natural history of Gadirtha fusca, a potential biological control agent of Chinese tallowtree (Triadica sebifera) in North America Gregory S. Wheeler1* , Emily Jones1, Kirsten Dyer1, Nick Silverson1 & Susan A. Wright2 1USDA/ARS Invasive Plant Research Laboratory, 3225 College Ave., Ft Lauderdale, FL 33314, USA, and 2USDA/ARS Invasive Plant Research Laboratory, Gainesville, FL 32608, USA Accepted: 23 August 2018 Key words: biocontrol, classical biological control, weed control, Euphorbiaceae, defoliating caterpillar, host range tests, invasive weeds, Sapium, Lepidoptera, Nolidae, integrated pest management, IPM Abstract Classical biological control can provide an ecologically sound, cost-effective, and sustainable manage- ment solution to protect diverse habitats. These natural and managed ecosystems are being invaded and transformed by invasive species. Chinese tallowtree, Triadica sebifera (L.) Small (Euphorbiaceae), is one of the most damaging invasive weeds in the southeastern USA, impacting wetlands, forests, and natural areas. A defoliating moth, Gadirtha fusca Pogue (Lepidoptera: Nolidae), was discovered feeding on Chinese tallowtree leaves in the weed’s native range and has been tested for its suitability as a biological control agent. Natural history studies of G. fusca indicated that the neonates have five instars and require 15.4 days to reach pupation. Complete development from egg hatch to adult emergence required 25.8 days. No differences were found between males and females in terms of life history and nutritional indices measured. Testing of the host range of G. fusca larvae was conducted with no-choice, dual-choice, and multigeneration tests and the results indicated that this species has a very narrow host range. -
Developmental Evolution of Endosperm in Basal Angiosperms: Evidence from Amborella Amborellaceae), Nuphar Nymphaeaceae), and Illicium Illiciaceae)
Plant Syst. Evol. 228: 153±169)2001) Developmental evolution of endosperm in basal angiosperms: evidence from Amborella Amborellaceae), Nuphar Nymphaeaceae), and Illicium Illiciaceae) S. K. Floyd and W. E. Friedman Department of Environmental, Population, and Organismic Biology, University of Colorado, Boulder, Colorado, USA Received January 19, 2001 Accepted March 19, 2001 Abstract. Because of their basal phylogenetic posi- Within the last two years remarkable progress tion, Amborella, Nymphaeales, and Illiciales )and has been made toward the resolution of deep allies) are key to reconstructing ancestral character angiosperm phylogenetic relationships. The states and to tracing character state transitions that results of several independent, molecular se- occurred during the earliest radiation of ¯owering quence-based analyses have converged on plants. Endosperm is the sexually-derived embryo- similar results for rooting the angiosperm tree nourishing tissue that is unique to the life cycle of and have identi®ed the three earliest-diverging angiosperms. We provide detailed descriptions of endosperm development in Amborella, Nuphar lineages of ¯owering plants )Mathews and )Nymphaeales), and Illicium )Illiciales) and com- Donoghue 1999; Parkinson et al. 1999; Qiu pare patterns within an explicit phylogenetic con- et al. 1999, 2000; Soltis et al. 1999, 2000; text for the three basal lineages that they represent. Borsch et al. 2000; Graham and Olmstead Amborella and Illicium share a bipolar, cellular 2000; Savolainen et al. 2000). The consensus of pattern of development, characterized by an these analyses is that Amborella trichopoda is oblique ®rst division, that was resolved as ancestral sistertoallotherextantangiosperms,Nymphae- for ¯owering plants. A series of character state ales )Nymphaeaceae plus Cabombaceae) is the transformations occurred within Nymphaeales sister group to all taxa except Amborella, and a which led ®rst to a modi®ed cellular pattern with clade including Illiciales, Austrobaileyaceae, a transverse ®rst division )present in Nuphar).