Evolutionary Relationships of the Arthropoda I
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
Species Concepts Should Not Conflict with Evolutionary History, but Often Do
ARTICLE IN PRESS Stud. Hist. Phil. Biol. & Biomed. Sci. xxx (2008) xxx–xxx Contents lists available at ScienceDirect Stud. Hist. Phil. Biol. & Biomed. Sci. journal homepage: www.elsevier.com/locate/shpsc Species concepts should not conflict with evolutionary history, but often do Joel D. Velasco Department of Philosophy, University of Wisconsin-Madison, 5185 White Hall, 600 North Park St., Madison, WI 53719, USA Department of Philosophy, Building 90, Stanford University, Stanford, CA 94305, USA article info abstract Keywords: Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts Biological Species Concept evolutionary history. While defences against this particular criticism have been attempted, I argue that Phylogenetic Species Concept these responses are unsuccessful. In addition, I argue that the source of this problem leads to previously Phylogenetic Trees unappreciated, and deeper, fatal objections. These objections to the BSC also straightforwardly apply to Taxonomy other species concepts that are not defined by genealogical history. What is missing from many previous discussions is the fact that the Tree of Life, which represents phylogenetic history, is independent of our choice of species concept. Some species concepts are consistent with species having unique positions on the Tree while others, including the BSC, are not. Since representing history is of primary importance in evolutionary biology, these problems lead to the conclusion that the BSC, along with many other species concepts, are unacceptable. If species are to be taxa used in phylogenetic inferences, we need a history- based species concept. Ó 2008 Elsevier Ltd. All rights reserved. When citing this paper, please use the full journal title Studies in History and Philosophy of Biological and Biomedical Sciences 1. -
Phylogenetic Trees and Cladograms Are Graphical Representations (Models) of Evolutionary History That Can Be Tested
AP Biology Lab/Cladograms and Phylogenetic Trees Name _______________________________ Relationship to the AP Biology Curriculum Framework Big Idea 1: The process of evolution drives the diversity and unity of life. Essential knowledge 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Learning Objectives: LO 1.17 The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram in order to (1) identify shared characteristics, (2) make inferences about the evolutionary history of the group, and (3) identify character data that could extend or improve the phylogenetic tree. LO 1.18 The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or a simple cladogram to determine evolutionary history and speciation. LO 1.19 The student is able create a phylogenetic tree or simple cladogram that correctly represents evolutionary history and speciation from a provided data set. [Introduction] Cladistics is the study of evolutionary classification. Cladograms show evolutionary relationships among organisms. Comparative morphology investigates characteristics for homology and analogy to determine which organisms share a recent common ancestor. A cladogram will begin by grouping organisms based on a characteristics displayed by ALL the members of the group. Subsequently, the larger group will contain increasingly smaller groups that share the traits of the groups before them. However, they also exhibit distinct changes as the new species evolve. Further, molecular evidence from genes which rarely mutate can provide molecular clocks that tell us how long ago organisms diverged, unlocking the secrets of organisms that may have similar convergent morphology but do not share a recent common ancestor. -
An Introduction to Phylogenetic Analysis
This article reprinted from: Kosinski, R.J. 2006. An introduction to phylogenetic analysis. Pages 57-106, in Tested Studies for Laboratory Teaching, Volume 27 (M.A. O'Donnell, Editor). Proceedings of the 27th Workshop/Conference of the Association for Biology Laboratory Education (ABLE), 383 pages. Compilation copyright © 2006 by the Association for Biology Laboratory Education (ABLE) ISBN 1-890444-09-X All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the copyright owner. Use solely at one’s own institution with no intent for profit is excluded from the preceding copyright restriction, unless otherwise noted on the copyright notice of the individual chapter in this volume. Proper credit to this publication must be included in your laboratory outline for each use; a sample citation is given above. Upon obtaining permission or with the “sole use at one’s own institution” exclusion, ABLE strongly encourages individuals to use the exercises in this proceedings volume in their teaching program. Although the laboratory exercises in this proceedings volume have been tested and due consideration has been given to safety, individuals performing these exercises must assume all responsibilities for risk. The Association for Biology Laboratory Education (ABLE) disclaims any liability with regards to safety in connection with the use of the exercises in this volume. The focus of ABLE is to improve the undergraduate biology laboratory experience by promoting the development and dissemination of interesting, innovative, and reliable laboratory exercises. -
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). -
Phylogenetic Definitions in the Pre-Phylocode Era; Implications for Naming Clades Under the Phylocode
PaleoBios 27(1):1–6, April 30, 2007 © 2006 University of California Museum of Paleontology Phylogenetic definitions in the pre-PhyloCode era; implications for naming clades under the PhyloCode MiChAel P. TAylor Palaeobiology research Group, School of earth and environmental Sciences, University of Portsmouth, Portsmouth Po1 3Ql, UK; [email protected] The last twenty years of work on phylogenetic nomenclature have given rise to many names and definitions that are now considered suboptimal. in formulating permanent definitions under the PhyloCode when it is implemented, it will be necessary to evaluate the corpus of existing names and make judgements about which to establish and which to discard. This is not straightforward, because early definitions are often inexplicit and ambiguous, generally do not meet the requirements of the PhyloCode, and in some cases may not be easily recognizable as phylogenetic definitions at all. recognition of synonyms is also complicated by the use of different kinds of specifiers (species, specimens, clades, genera, suprageneric rank-based names, and vernacular names) and by definitions whose content changes under different phylogenetic hypotheses. in light of these difficulties, five principles are suggested to guide the interpreta- tion of pre-PhyloCode clade-names and to inform the process of naming clades under the PhyloCode: (1) do not recognize “accidental” definitions; (2) malformed definitions should be interpreted according to the intention of the author when and where this is obvious; (3) apomorphy-based and other definitions must be recognized as well as node-based and stem-based definitions; (4) definitions using any kind of specifier taxon should be recognized; and (5) priority of synonyms and homonyms should guide but not prescribe. -
Lineages, Splits and Divergence Challenge Whether the Terms Anagenesis and Cladogenesis Are Necessary
Biological Journal of the Linnean Society, 2015, , – . With 2 figures. Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary FELIX VAUX*, STEVEN A. TREWICK and MARY MORGAN-RICHARDS Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand Received 3 June 2015; revised 22 July 2015; accepted for publication 22 July 2015 Using the framework of evolutionary lineages to separate the process of evolution and classification of species, we observe that ‘anagenesis’ and ‘cladogenesis’ are unnecessary terms. The terms have changed significantly in meaning over time, and current usage is inconsistent and vague across many different disciplines. The most popular definition of cladogenesis is the splitting of evolutionary lineages (cessation of gene flow), whereas anagenesis is evolutionary change between splits. Cladogenesis (and lineage-splitting) is also regularly made synonymous with speciation. This definition is misleading as lineage-splitting is prolific during evolution and because palaeontological studies provide no direct estimate of gene flow. The terms also fail to incorporate speciation without being arbitrary or relative, and the focus upon lineage-splitting ignores the importance of divergence, hybridization, extinction and informative value (i.e. what is helpful to describe as a taxon) for species classification. We conclude and demonstrate that evolution and species diversity can be considered with greater clarity using simpler, more transparent terms than anagenesis and cladogenesis. Describing evolution and taxonomic classification can be straightforward, and there is no need to ‘make words mean so many different things’. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000. -
Phylogeny Codon Models • Last Lecture: Poor Man’S Way of Calculating Dn/Ds (Ka/Ks) • Tabulate Synonymous/Non-Synonymous Substitutions • Normalize by the Possibilities
Phylogeny Codon models • Last lecture: poor man’s way of calculating dN/dS (Ka/Ks) • Tabulate synonymous/non-synonymous substitutions • Normalize by the possibilities • Transform to genetic distance KJC or Kk2p • In reality we use codon model • Amino acid substitution rates meet nucleotide models • Codon(nucleotide triplet) Codon model parameterization Stop codons are not allowed, reducing the matrix from 64x64 to 61x61 The entire codon matrix can be parameterized using: κ kappa, the transition/transversionratio ω omega, the dN/dS ratio – optimizing this parameter gives the an estimate of selection force πj the equilibrium codon frequency of codon j (Goldman and Yang. MBE 1994) Empirical codon substitution matrix Observations: Instantaneous rates of double nucleotide changes seem to be non-zero There should be a mechanism for mutating 2 adjacent nucleotides at once! (Kosiol and Goldman) • • Phylogeny • • Last lecture: Inferring distance from Phylogenetic trees given an alignment How to infer trees and distance distance How do we infer trees given an alignment • • Branch length Topology d 6-p E 6'B o F P Edo 3 vvi"oH!.- !fi*+nYolF r66HiH- .) Od-:oXP m a^--'*A ]9; E F: i ts X o Q I E itl Fl xo_-+,<Po r! UoaQrj*l.AP-^PA NJ o - +p-5 H .lXei:i'tH 'i,x+<ox;+x"'o 4 + = '" I = 9o FF^' ^X i! .poxHo dF*x€;. lqEgrE x< f <QrDGYa u5l =.ID * c 3 < 6+6_ y+ltl+5<->-^Hry ni F.O+O* E 3E E-f e= FaFO;o E rH y hl o < H ! E Y P /-)^\-B 91 X-6p-a' 6J. -
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography of Rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus)
City University of New York (CUNY) CUNY Academic Works Publications and Research New York City College of Technology 2016 Diversity-dependent cladogenesis throughout western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) Christopher Blair CUNY New York City College of Technology Santiago Sánchez-Ramírez University of Toronto How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/ny_pubs/344 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] 1Blair, C., Sánchez-Ramírez, S., 2016. Diversity-dependent cladogenesis throughout 2 western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: 3 Crotalus and Sistrurus ). Molecular Phylogenetics and Evolution 97, 145–154. 4 https://doi.org/10.1016/j.ympev.2015.12.020. © 2016. This manuscript version is made 5 available under the CC-BY-NC-ND 4.0 license. 6 7 8 Diversity-dependent cladogenesis throughout western Mexico: evolutionary 9 biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) 10 11 12 CHRISTOPHER BLAIR1*, SANTIAGO SÁNCHEZ-RAMÍREZ2,3,4 13 14 15 1Department of Biological Sciences, New York City College of Technology, Biology PhD 16 Program, Graduate Center, The City University of New York, 300 Jay Street, Brooklyn, 17 NY 11201, USA. 18 2Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks 19 Street, Toronto, ON, M5S 3B2, Canada. 20 3Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, 21 ON, M5S 2C6, Canada. 22 4Present address: Environmental Genomics Group, Max Planck Institute for 23 Evolutionary Biology, August-Thienemann-Str. -
Phylogenomic Resolution of Sea Spider Diversification Through Integration Of
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.31.929612; this version posted February 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Phylogenomic resolution of sea spider diversification through integration of multiple data classes 1Jesús A. Ballesteros†, 1Emily V.W. Setton†, 1Carlos E. Santibáñez López†, 2Claudia P. Arango, 3Georg Brenneis, 4Saskia Brix, 5Esperanza Cano-Sánchez, 6Merai Dandouch, 6Geoffrey F. Dilly, 7Marc P. Eleaume, 1Guilherme Gainett, 8Cyril Gallut, 6Sean McAtee, 6Lauren McIntyre, 9Amy L. Moran, 6Randy Moran, 5Pablo J. López-González, 10Gerhard Scholtz, 6Clay Williamson, 11H. Arthur Woods, 12Ward C. Wheeler, 1Prashant P. Sharma* 1 Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI, USA 2 Queensland Museum, Biodiversity Program, Brisbane, Australia 3 Zoologisches Institut und Museum, Cytologie und Evolutionsbiologie, Universität Greifswald, Greifswald, Germany 4 Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), c/o Biocenter Grindel (CeNak), Martin-Luther-King-Platz 3, Hamburg, Germany 5 Biodiversidad y Ecología Acuática, Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain 6 Department of Biology, California State University-Channel Islands, Camarillo, CA, USA 7 Départment Milieux et Peuplements Aquatiques, Muséum national d’Histoire naturelle, Paris, France 8 Institut de Systématique, Emvolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Concarneau, France 9 Department of Biology, University of Hawai’i at Mānoa, Honolulu, HI, USA Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.31.929612; this version posted February 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
A Phylogenetic Analysis of the Basal Ornithischia (Reptilia, Dinosauria)
A PHYLOGENETIC ANALYSIS OF THE BASAL ORNITHISCHIA (REPTILIA, DINOSAURIA) Marc Richard Spencer A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements of the degree of MASTER OF SCIENCE December 2007 Committee: Margaret M. Yacobucci, Advisor Don C. Steinker Daniel M. Pavuk © 2007 Marc Richard Spencer All Rights Reserved iii ABSTRACT Margaret M. Yacobucci, Advisor The placement of Lesothosaurus diagnosticus and the Heterodontosauridae within the Ornithischia has been problematic. Historically, Lesothosaurus has been regarded as a basal ornithischian dinosaur, the sister taxon to the Genasauria. Recent phylogenetic analyses, however, have placed Lesothosaurus as a more derived ornithischian within the Genasauria. The Fabrosauridae, of which Lesothosaurus was considered a member, has never been phylogenetically corroborated and has been considered a paraphyletic assemblage. Prior to recent phylogenetic analyses, the problematic Heterodontosauridae was placed within the Ornithopoda as the sister taxon to the Euornithopoda. The heterodontosaurids have also been considered as the basal member of the Cerapoda (Ornithopoda + Marginocephalia), the sister taxon to the Marginocephalia, and as the sister taxon to the Genasauria. To reevaluate the placement of these taxa, along with other basal ornithischians and more derived subclades, a phylogenetic analysis of 19 taxonomic units, including two outgroup taxa, was performed. Analysis of 97 characters and their associated character states culled, modified, and/or rescored from published literature based on published descriptions, produced four most parsimonious trees. Consistency and retention indices were calculated and a bootstrap analysis was performed to determine the relative support for the resultant phylogeny. The Ornithischia was recovered with Pisanosaurus as its basalmost member.