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Ecological Correlates of Ghost Lineages in Ruminants
Paleobiology, 38(1), 2012, pp. 101–111 Ecological correlates of ghost lineages in ruminants Juan L. Cantalapiedra, Manuel Herna´ndez Ferna´ndez, Gema M. Alcalde, Beatriz Azanza, Daniel DeMiguel, and Jorge Morales Abstract.—Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation. Juan L. Cantalapiedra, Gema Alcalde, and Jorge Morales. Departamento de Paleobiologı´a, Museo Nacional de Ciencias Naturales, UCM-CSIC, Pinar 25, 28006 Madrid, Spain. E-mail: [email protected] Manuel Herna´ndez Ferna´ndez. Departamento de Paleontologı´a, Facultad de Ciencias Geolo´gicas, Universidad Complutense de Madrid y Departamento de Cambio Medioambiental, Instituto de Geociencias, Consejo Superior de Investigaciones Cientı´ficas, Jose´ Antonio Novais 2, 28040 Madrid, Spain Daniel DeMiguel. -
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 . -
Die Microsauria Des Mitteleuropäischen Rotliegend
Die Microsauria des mitteleuropäischen Rotliegend Dissertation zur Erlangung des Grades „Doktor der Naturwissenschaften" im Promotionsfach Geologie/Paläontologie am Fachbereich Chemie, Pharmazie und Geowissenschaften der Johannes Gutenberg-Universität in Mainz Sabine Glienke geb. in Worms Mainz, 2011 http://d-nb.info/1058187503 Inhalt Inhalt 1. Einleitung 6 1.1. Allgemeine Merkmale und Bearbeitungsgeschichte 6 1.2. Fundorte und Erhaltung 9 2. Methoden, Abkürzungen und Material 16 2.1. Methoden 16 2.1.1. Bearbeitung der Skelette 16 2.1.2. Gewinnung und Bearbeitung der Einzelknochen 16 2.1.3. Kladogramme 17 2.2. Abkürzungen 17 2.2.1. Sammlungen 17 2.2.2. In den Zeichnungen verwendete Abkürzungen 17 2.3. Übersicht über die untersuchten Skelette 19 3. Beschreibungen 21 3.1. Die Familie Brachystelechidae CARROLL& GASKILL, 1978 21 3.1.1. Systematische Stellung 21 3.1.2. Diagnose 21 3.2. Die Gattung Batropetes CARROLL & GASKILL, 1971 21 3.2.1. Systematische Stellung 21 3.2.2. Diagnose 22 3.2.3. Die vier Spezies der Gattung Batropetes 22 3.3. Batropetes niederkirchensis n. sp 26 3.3.1. Diagnose 26 3.3.2. Beschreibung 28 3.3.2.1. Schädel 28 3.3.2.1.1. Schädeldach 28 3.3.2.1.2. Gaumen 38 3.3.2.1.3. Hirnkapsel 43 3.3.2.1.4. Unterkiefer 46 3.3.2.2. Postcraniales Skelett 48 Inhalt 3.4. Batropetes palatinus n. sp 62 3.4.1. Diagnose 62 3.4.2. Beschreibung 63 3.4.2.1. Schädel 74 3.4.2.1.1. Schädeldach 74 3.4.2.1.2. -
Phylogeny of a Rapidly Evolving Clade: the Cichlid Fishes of Lake Malawi
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 5107–5110, April 1999 Evolution Phylogeny of a rapidly evolving clade: The cichlid fishes of Lake Malawi, East Africa (adaptive radiationysexual selectionyspeciationyamplified fragment length polymorphismylineage sorting) R. C. ALBERTSON,J.A.MARKERT,P.D.DANLEY, AND T. D. KOCHER† Department of Zoology and Program in Genetics, University of New Hampshire, Durham, NH 03824 Communicated by John C. Avise, University of Georgia, Athens, GA, March 12, 1999 (received for review December 17, 1998) ABSTRACT Lake Malawi contains a flock of >500 spe- sponsible for speciation, then we expect that sister taxa will cies of cichlid fish that have evolved from a common ancestor frequently differ in color pattern but not morphology. within the last million years. The rapid diversification of this Most attempts to determine the relationships among cichlid group has been attributed to morphological adaptation and to species have used morphological characters, which may be sexual selection, but the relative timing and importance of prone to convergence (8). Molecular sequences normally these mechanisms is not known. A phylogeny of the group provide the independent estimate of phylogeny needed to infer would help identify the role each mechanism has played in the evolutionary mechanisms. The Lake Malawi cichlids, however, evolution of the flock. Previous attempts to reconstruct the are speciating faster than alleles can become fixed within a relationships among these taxa using molecular methods have species (9, 10). The coalescence of mtDNA haplotypes found been frustrated by the persistence of ancestral polymorphisms within populations predates the origin of many species (11). In within species. -
Major Clades of Agaricales: a Multilocus Phylogenetic Overview
Mycologia, 98(6), 2006, pp. 982–995. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 Major clades of Agaricales: a multilocus phylogenetic overview P. Brandon Matheny1 Duur K. Aanen Judd M. Curtis Laboratory of Genetics, Arboretumlaan 4, 6703 BD, Biology Department, Clark University, 950 Main Street, Wageningen, The Netherlands Worcester, Massachusetts, 01610 Matthew DeNitis Vale´rie Hofstetter 127 Harrington Way, Worcester, Massachusetts 01604 Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708 Graciela M. Daniele Instituto Multidisciplinario de Biologı´a Vegetal, M. Catherine Aime CONICET-Universidad Nacional de Co´rdoba, Casilla USDA-ARS, Systematic Botany and Mycology de Correo 495, 5000 Co´rdoba, Argentina Laboratory, Room 304, Building 011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350 Dennis E. Desjardin Department of Biology, San Francisco State University, Jean-Marc Moncalvo San Francisco, California 94132 Centre for Biodiversity and Conservation Biology, Royal Ontario Museum and Department of Botany, University Bradley R. Kropp of Toronto, Toronto, Ontario, M5S 2C6 Canada Department of Biology, Utah State University, Logan, Utah 84322 Zai-Wei Ge Zhu-Liang Yang Lorelei L. Norvell Kunming Institute of Botany, Chinese Academy of Pacific Northwest Mycology Service, 6720 NW Skyline Sciences, Kunming 650204, P.R. China Boulevard, Portland, Oregon 97229-1309 Jason C. Slot Andrew Parker Biology Department, Clark University, 950 Main Street, 127 Raven Way, Metaline Falls, Washington 99153- Worcester, Massachusetts, 01609 9720 Joseph F. Ammirati Else C. Vellinga University of Washington, Biology Department, Box Department of Plant and Microbial Biology, 111 355325, Seattle, Washington 98195 Koshland Hall, University of California, Berkeley, California 94720-3102 Timothy J. -
Stuttgarter Beiträge Zur Naturkunde
S^5 ( © Biodiversity Heritage Library, http://www.biodiversitylibrary.org/; www.zobodat.at Stuttgarter Beiträge zur Naturkunde Serie B (Geologie und Paläontologie) Herausgeber: Staatliches Museum für Naturkunde, Rosenstein 1, D-70191 Stuttgart Stuttgarter Beitr. Naturk. Ser. B Nr. 278 175 pp., 4pls., 54figs. Stuttgart, 30. 12. 1999 Comparative osteology oi Mastodonsaurus giganteus (Jaeger, 1828) from the Middle Triassic (Lettenkeuper: Longobardian) of Germany (Baden-Württemberg, Bayern, Thüringen) By Rainer R. Schoch, Stuttgart With 4 plates and 54 textfigures Abstract Mastodonsaurus giganteus, the most abundant and giant amphibian of the German Letten- keuper, is revised. The study is based on the excellently preserved and very rieh material which was excavated during road construction in 1977 near Kupferzeil, Northern Baden- Württemberg. It is shown that there exists only one diagnosable species of Mastodonsaurus, to which all Lettenkeuper material can be attributed. All finds from other horizons must be referred to as Mastodonsauridae gen. et sp. indet. because of their fragmentary Status. A sec- ond, definitely diagnostic genus of this family is Heptasaurus from the higher Middle and Upper Buntsandstein. Finally a diagnosis of the family Mastodonsauridae is provided. Ä detailed osteological description of Mastodonsaurus giganteus reveals numerous un- known or formerly inadequately understood features, yielding data on various hitherto poor- ly known regions of the skeleton. The sutures of the skull roof, which could be studied in de- tail, are significantly different from the schemes presented by previous authors. The endocra- nium and mandible are further points of particular interest. The palatoquadrate contributes a significant part to the formation of the endocranium by an extensive and complicated epi- pterygoid. -
Tetrapod Biostratigraphy and Biochronology of the Triassic–Jurassic Transition on the Southern Colorado Plateau, USA
Palaeogeography, Palaeoclimatology, Palaeoecology 244 (2007) 242–256 www.elsevier.com/locate/palaeo Tetrapod biostratigraphy and biochronology of the Triassic–Jurassic transition on the southern Colorado Plateau, USA Spencer G. Lucas a,⁎, Lawrence H. Tanner b a New Mexico Museum of Natural History, 1801 Mountain Rd. N.W., Albuquerque, NM 87104-1375, USA b Department of Biology, Le Moyne College, 1419 Salt Springs Road, Syracuse, NY 13214, USA Received 15 March 2006; accepted 20 June 2006 Abstract Nonmarine fluvial, eolian and lacustrine strata of the Chinle and Glen Canyon groups on the southern Colorado Plateau preserve tetrapod body fossils and footprints that are one of the world's most extensive tetrapod fossil records across the Triassic– Jurassic boundary. We organize these tetrapod fossils into five, time-successive biostratigraphic assemblages (in ascending order, Owl Rock, Rock Point, Dinosaur Canyon, Whitmore Point and Kayenta) that we assign to the (ascending order) Revueltian, Apachean, Wassonian and Dawan land-vertebrate faunachrons (LVF). In doing so, we redefine the Wassonian and the Dawan LVFs. The Apachean–Wassonian boundary approximates the Triassic–Jurassic boundary. This tetrapod biostratigraphy and biochronology of the Triassic–Jurassic transition on the southern Colorado Plateau confirms that crurotarsan extinction closely corresponds to the end of the Triassic, and that a dramatic increase in dinosaur diversity, abundance and body size preceded the end of the Triassic. © 2006 Elsevier B.V. All rights reserved. Keywords: Triassic–Jurassic boundary; Colorado Plateau; Chinle Group; Glen Canyon Group; Tetrapod 1. Introduction 190 Ma. On the southern Colorado Plateau, the Triassic– Jurassic transition was a time of significant changes in the The Four Corners (common boundary of Utah, composition of the terrestrial vertebrate (tetrapod) fauna. -
Morphology, Phylogeny, and Evolution of Diadectidae (Cotylosauria: Diadectomorpha)
Morphology, Phylogeny, and Evolution of Diadectidae (Cotylosauria: Diadectomorpha) by Richard Kissel A thesis submitted in conformity with the requirements for the degree of doctor of philosophy Graduate Department of Ecology & Evolutionary Biology University of Toronto © Copyright by Richard Kissel 2010 Morphology, Phylogeny, and Evolution of Diadectidae (Cotylosauria: Diadectomorpha) Richard Kissel Doctor of Philosophy Graduate Department of Ecology & Evolutionary Biology University of Toronto 2010 Abstract Based on dental, cranial, and postcranial anatomy, members of the Permo-Carboniferous clade Diadectidae are generally regarded as the earliest tetrapods capable of processing high-fiber plant material; presented here is a review of diadectid morphology, phylogeny, taxonomy, and paleozoogeography. Phylogenetic analyses support the monophyly of Diadectidae within Diadectomorpha, the sister-group to Amniota, with Limnoscelis as the sister-taxon to Tseajaia + Diadectidae. Analysis of diadectid interrelationships of all known taxa for which adequate specimens and information are known—the first of its kind conducted—positions Ambedus pusillus as the sister-taxon to all other forms, with Diadectes sanmiguelensis, Orobates pabsti, Desmatodon hesperis, Diadectes absitus, and (Diadectes sideropelicus + Diadectes tenuitectes + Diasparactus zenos) representing progressively more derived taxa in a series of nested clades. In light of these results, it is recommended herein that the species Diadectes sanmiguelensis be referred to the new genus -
Early Tetrapod Relationships Revisited
Biol. Rev. (2003), 78, pp. 251–345. f Cambridge Philosophical Society 251 DOI: 10.1017/S1464793102006103 Printed in the United Kingdom Early tetrapod relationships revisited MARCELLO RUTA1*, MICHAEL I. COATES1 and DONALD L. J. QUICKE2 1 The Department of Organismal Biology and Anatomy, The University of Chicago, 1027 East 57th Street, Chicago, IL 60637-1508, USA ([email protected]; [email protected]) 2 Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire SL57PY, UK and Department of Entomology, The Natural History Museum, Cromwell Road, London SW75BD, UK ([email protected]) (Received 29 November 2001; revised 28 August 2002; accepted 2 September 2002) ABSTRACT In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relation- ships, we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod clades. A stem-based (total-group) definition of Tetrapoda is preferred over apomorphy- and node-based (crown-group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP* search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differ- ences between these trees concern: (1) the internal relationships of aı¨stopods, the three selected species of which form a trichotomy; (2) the internal relationships of embolomeres, with Archeria -
Phylogeny of Basal Tetrapoda
Stuart S. Sumida Biology 342 Phylogeny of Basal Tetrapoda The group of bony fishes that gave rise to land-dwelling vertebrates and their descendants (Tetrapoda, or colloquially, “tetrapods”) was the lobe-finned fishes, or Sarcopterygii. Sarcoptrygii includes coelacanths (which retain one living form, Latimeria), lungfish, and crossopterygians. The transition from sarcopterygian fishes to stem tetrapods proceeded through a series of groups – not all of which are included here. There was no sharp and distinct transition, rather it was a continuum from very tetrapod-like fishes to very fish-like tetrapods. SARCOPTERYGII – THE LOBE-FINNED FISHES Includes •Actinista (including Coelacanths) •Dipnoi (lungfishes) •Crossopterygii Crossopterygians include “tetrapods” – 4- legged land-dwelling vertebrates. The Actinista date back to the Devonian. They have very well developed lobed-fins. There remains one livnig representative of the group, the coelacanth, Latimeria chalumnae. A lungfish The Crossopterygii include numerous representatives, the best known of which include Eusthenopteron (pictured here) and Panderichthyes. Panderichthyids were the most tetrapod-like of the sarcopterygian fishes. Panderichthyes – note the lack of dorsal fine, but retention of tail fin. Coelacanths Lungfish Rhizodontids Eusthenopteron Panderichthyes Tiktaalik Ventastega Acanthostega Ichthyostega Tulerpeton Whatcheeria Pederpes More advanced amphibians Tiktaalik roseae – a lobe-finned fish intermediate between typical sarcopterygians and basal tetrapods. Mid to Late Devonian; 375 million years old. The back end of Tiktaalik’s skull is intermediate between fishes and tetrapods. Tiktaalik is a fish with wrist bones, yet still retaining fin rays. The posture of Tiktaalik’s fin/limb is intermediate between that of fishes an tetrapods. Coelacanths Lungfish Rhizodontids Eusthenopteron Panderichthyes Tiktaalik Ventastega Acanthostega Ichthyostega Tulerpeton Whatcheeria Pederpes More advanced amphibians Reconstructions of the basal tetrapod Ventastega. -
From Sea to Slime: Evolution of Amphibians Late Devonian: Rhipidistians an Important Link: Tooth Structure Skeletal Modification
Late Devonian: Rhipidistians From Sea to Slime: Evolution of Amphibians Lungs were developed in two groups of lobe-finned fishes - Rhipidistians and lungfishes . The Rhipidistians are considered to be the ultimate ancestors of later land animals. Rhipidistians such as Eusthenopteron had evolved "land animal-like features": Eusthenopteron Skeletal Modifications An Important Link: Tooth Structure Labyrinthodont tooth Labyrinthodont tooth of Rhipidistian fish of early amphibian (Eusthenopteron) (Archegosaurus) Labyrinthodont tooth structure (with complexly infolded enamel) is shared between Rhipidistian fishes and the earliest amphibians. This strongly supports a close relationship between the two groups. 1 Late Devonian: Ichthyostega and Acanthostega -Ichthyostega was a cross between a fish and an amphibian -Ichthyostega had legs and walked and was a true tetrapod. -With true legs, it could live on land for extended periods. -The primitive amphibians like Ichthyostega had a special kind of skin that helped them retain bodily fluids and deter desiccation. -Stronger skeletons allowed the primitive amphibians to live more comfortably with the increased gravity on land. -Animals like Ichthyostega used their limbs for locomotion and their tails for balance. Ichthyostega Carboniferous to Permian Evolution of neck and ear · Amphibian nostrils became increasingly functional for breathing air. · Amphibians evolved "hands" and "feet" with five digits. · Amphibian tails became reduced in size. · Amphibian backbones grew stronger (this enabled amphibian bodies to grow bigger). · Amphibians obtained eardrums. -Fishes need limbs to support bodies and ears to hear sounds in the air. -Fins changed to limbs -Several bones of the skull changed to the shoulder bones -Tongue cartilage (part of the jaw in fish) became an ear bone. -
Palate Anatomy and Morphofunctional Aspects of Interpterygoid Vacuities in Temnospondyl Cranial Evolution
Lautenschlager, S., Witzmann, F., & Werneburg, I. (2016). Palate anatomy and morphofunctional aspects of interpterygoid vacuities in temnospondyl cranial evolution. Naturwissenschaften, 103, [79]. https://doi.org/10.1007/s00114-016-1402-z Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.1007/s00114-016-1402-z Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via Springer at http://link.springer.com/article/10.1007/s00114-016-1402-z. Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ Sci Nat (2016) 103:79 DOI 10.1007/s00114-016-1402-z ORIGINAL PAPER Palate anatomy and morphofunctional aspects of interpterygoid vacuities in temnospondyl cranial evolution Stephan Lautenschlager1 & Florian Witzmann2,3 & Ingmar Werneburg3,4,5 Received: 19 April 2016 /Revised: 1 August 2016 /Accepted: 23 August 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Temnospondyls were the morphologically and tax- significance. Here, we applied finite element analysis, to test onomically most diverse group of early tetrapods with a near- the possibility that the interpterygoid vacuities served for global distribution during the Palaeozoic and Mesozoic. stress distribution during contraction of the jaw closing mus- Members of this group occupied a range of different habitats culature.