DOCSLIB.ORG

Systematics - BIO 615

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Systematics - BIO 615 Systematics - BIO 615 Outline - History and introduction to phylogenetic inference 1. Pre Lamarck, Pre Darwin “Classification without phylogeny” 2. Lamarck & Darwin to Hennig (et al.) “Classification with phylogeny but without a reproducible method” 3. Hennig (et al.) to today “Classification with phylogeny & a reproducible method” Biosystematics History alpha phylogenetics Aristotle - Scala Naturae - ladder of perfection with humans taxonomy at top - DIFFICULT mental concept to dislodge! (use of terms like “higher” and “lower” for organisms persist) character identification evolution Linnaeus - perpetuated the ladder-like view of life linear, pre evolution descriptions phylogeny 1758 - Linnaeus grouped all animals into 6 higher taxa: 1. Mammals ( top ) 2. Birds collections classification biogeography 3. Reptiles 4. Fishes 5. Insects Describing taxa = assigning names to groups (populations) 6. Worms ( bottom ) = classification Outline - History and introduction to History phylogenetic inference Lamarck - 1800 - Major impact on Biology: 1. Pre Lamarck, Pre Darwin - First public account of evolution - proposed that modern species had descended from common ancestors over “Classification without phylogeny” immense periods of time - Radical! evolution = descent with modification 2. Lamarck & Darwin to Hennig (et al.) - Began with a ladder-like description… but considered “Classification with phylogeny but Linnaeus’s “worms” to be a chaotic “wastebucket” without a reproducible method” taxon 3. Hennig (et al.) to today - He raided the worm group to liberate disparate taxa “Classification with phylogeny & a - Early and MAJOR example of using data interpreted reproducible method” within an evolutionary framework to classify 1 Systematics - BIO 615 History Lamarck, J. B. 1809. Philosophie Zoologique History Perhaps the first branching diagram, “phylogentic tree” - Phylogenetics began before “evolutionary trees” published in the history of Biology - 1809 - Classifications were taken as proxies - representations of the “natural order,” these were the “trees” Lamarck’s ideas: - By putting taxa together in a group, one was saying Two origins of life (since both “these taxa are closer to one another than to were “equally primitive”) anything else - they belong together” Insects et al - side branch - “Closer” meant different things to different workers: e.g. Greater body form similarity / complexity Removed birds to side branch e.g. Greater evolutionary relationship rather than “below” mammals e.g. more shared homologies… (natural vs artificial) Lamarck, J. B. 1809. Philosophie Zoologique Biosystematics History alpha phylogenetics “Dans sa production des differents animaux, la taxonomy nature n'a pas execute une serie unique et character simple.” identification evolution (In its production of the different animals, descriptions phylogeny nature has not fashioned a single and simple series.) 1809 collections classification biogeography - Lamarck 1815 Phylogenetics began with the emergence of the idea of = the beginning of the end of the Scala evolution applied to classification Naturae 2 Systematics - BIO 615 History History Charles Darwin (& Alfred Russel Wallace) - “In regard to classification and all the endless disputes about the "Natural System," which no two authors define provided the mechanism (natural selection) to in the same way, I believe it ought, in accordance to my explain evolution - 1858 & 1859 heterodox notions, to be simply genealogical. Lamarck’s ideas, which lacked an accurate But as we have no written pedigrees you will, perhaps, say this will not help much; but I think it ultimately will, whenever mechanism, hadn’t spread heterodoxy becomes orthodoxy, for it will clear away an immense amount of rubbish about the value of characters, Darwin’s ideas did… and will make the difference between analogy and homology clear. The time will come, I believe, though I shall not live to see it, when we shall have very fairly true genealogical (That evolution occurred was apparent to many trees of each great kingdom of Nature.” who knew the fossil record, the problem, was “How?”) Darwin in a letter to Huxley, 1857 History History Classifications (starting in the mid to late 1800s) - Based on inferred evolutionary history - End of artificial classifications for convenience or for understanding the creator - But, “How does one infer evolutionary history?” no reproducible method, yet, to do so… Darwin (1859) On the Origin of Species History History Ernst Haeckel (late 1800s) The “method” of phylogenetic inference - Heavy supporter of (from which one may or may not derive a evolution, but not Darwin classification) that developed is referred to - “Ontogeny recapitulates as phylogeny” - not a law, as he thought Evolutionary Taxonomy - Coined terms: Ecology - spanned from the 1800s to the 1960s Phylum Phylogeny (1866) monophyletic - formed the “roots” of the discipline of polyphyletic phylogenetics 3 Systematics - BIO 615 History History Evolutionary Taxonomy (<1960s) Evolutionary Taxonomy (<1960s) - “Method” involved a reliance on - During the modern synthesis authority, not reproducible: systematics was marginalized “not a science” - Leading figures: Mayr & Simpson 1940s 1. Spend a lifetime learning as much as - Without a reproducible method, possible about the biology of a group hypotheses couldn’t be tested (morphology, development, fossils, etc.) 2. Publish a drawing of a phylogeny - No longer used, but exists in some forms based on one’s (informed) opinion today (in contrast to systematists who know nothing about their organisms!) = “Guessograms” Haeckel, 1872 - tree depicts 1) relationships, 2) timing of Haeckel, 1872 - tree lacks: 1) data? Characters supporting branching events, 3) diversity of groups through time branches? 2) quantification of support - strength of argument History Summary of contributions Evolutionary Taxonomy (<1960s) Good: “Know your organisms” Bad: not reproducible; no objective method; arbitrary, intuitive, no way to ET - many hypotheses generated, but no method to test. resolve conflicts Modern methods to test show many of the relationships to be “good”, or at least close… but many also rejected 4 Systematics - BIO 615 Outline - History and introduction to Lack of a reproducible method resulted in three phylogenetic inference major approaches: (Explosion in 1960s) 1. Pre Lamarck, Pre Darwin 1. Phenetics - similarity / distances only, not “Classification without phylogeny” evolution, not phylogeny, no weighting 2. Lamarck & Darwin to Hennig (et al.) 2. Cladistics - phylogeny inferred using “Classification with phylogeny but characters & parsimony without a reproducible method” 3. Hennig (et al.) to today 3. Statistical Phylogenetics - phylogeny “Classification with phylogeny & a inferred using corrected data & “best fitting reproducible method” model” History Phenetics - similarity only, not evolution, not phylogeny (1950-1960) - computerized, reproducible, “objective,” modern, sexy… - goal to remove all subjectivity, measure everything, use matrix of distances - sometimes called “Numerical Taxonomy” after book by Sokal & Sneath (1963) - cluster based on overall similarity - not evolutionary trees, but phenograms 1957 - first numerical phylogeny published (Michener & Sokal) History Phenetics - Problems Similarity sometimes reflects evolution… 1. Reproducible but no agreement on which clustering algorithm or statistic to use… Rhino Beetle Butterfly - different algorithms = different trees e.g. UPGMA, PCA… etc. True tree: - although there is only one true evolutionary tree, there are many alternative Butterfly Butterfly ‘similarity’ trees depending on the data & algorithm used Beetle Beetle 2. Similarity doesn’t always = evolutionary Rhino Rhino relationship! Phenogram Cladogram 5 Systematics - BIO 615 History And sometimes doesn’t… Phenetics - the good 1. Demanded explicit character analysis & laid Lizard Crocodile Bird groundwork for numerical phylogenetics True tree: 2. Still used for lower-level problems e.g. morphometrics, species demarcations… 3. And some higher-level problems Lizard Lizard Crocodile Crocodile Survives in various forms - an issue of debate… (see lecture on Distance methods) Bird Bird Phenogram Cladogram Definition - Phenetics Lack of a reproducible method resulted in three major approaches: Phenetics as originally applied, by Cain and Harrison (1960), refers to the "arrangement by overall 1. Phenetics - similarity / distances only, not similarity, based on all available characters without evolution, not phylogeny any weighting ...since it employs all observable characters (including of course genetic data when available)". 2. Cladistics - phylogeny inferred using characters & parsimony Cain, A. J., Harrison, G.A. (1960) Phyletic weighting. Proceedings of the Zoological Society of London 3. Statistical Phylogenetics - phylogeny 131: 1-31 inferred using corrected data & “best fitting model” History History Cladistics Cladistics 1950 - Willi Hennig “Grundzüge einer Theorie der - method explicit, reproducible phylogenetischen Systematik” - hypotheses of phylogeny could now be “tested” - German entomologist of Diptera - Hennig’s original method: - 1966 English translation of Phylogenetic 1. Distinguish homologies from analogies Systematics 2. Distinguish derived homologies - key: distinguish derived from (apomorphies) from ancestral ancestral homology (plesiomorphies) homologies - yields phylogenetic tree 3. Tree then built from apomorphies (evidence of common ancestry) - Vitriolic attacks
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 .
    [Show full text]
  • In Defence of the Three-Domains of Life Paradigm P.T.S
    van der Gulik et al. BMC Evolutionary Biology (2017) 17:218 DOI 10.1186/s12862-017-1059-z REVIEW Open Access In defence of the three-domains of life paradigm P.T.S. van der Gulik1*, W.D. Hoff2 and D. Speijer3* Abstract Background: Recently, important discoveries regarding the archaeon that functioned as the “host” in the merger with a bacterium that led to the eukaryotes, its “complex” nature, and its phylogenetic relationship to eukaryotes, have been reported. Based on these new insights proposals have been put forward to get rid of the three-domain Model of life, and replace it with a two-domain model. Results: We present arguments (both regarding timing, complexity, and chemical nature of specific evolutionary processes, as well as regarding genetic structure) to resist such proposals. The three-domain Model represents an accurate description of the differences at the most fundamental level of living organisms, as the eukaryotic lineage that arose from this unique merging event is distinct from both Archaea and Bacteria in a myriad of crucial ways. Conclusions: We maintain that “a natural system of organisms”, as proposed when the three-domain Model of life was introduced, should not be revised when considering the recent discoveries, however exciting they may be. Keywords: Eucarya, LECA, Phylogenetics, Eukaryogenesis, Three-domain model Background (English: domain) as a higher taxonomic level than The discovery that methanogenic microbes differ funda- regnum: introducing the three domains of cellular life, Ar- mentally from Bacteria such as Escherichia coli or Bacillus chaea, Bacteria and Eucarya. This paradigm was proposed subtilis constitutes one of the most important biological by Woese, Kandler and Wheelis in PNAS in 1990 [2].
    [Show full text]
  • Phylogenetics Topic 2: Phylogenetic and Genealogical Homology
    Phylogenetics Topic 2: Phylogenetic and genealogical homology Phylogenies distinguish homology from similarity Previously, we examined how rooted phylogenies provide a framework for distinguishing similarity due to common ancestry (HOMOLOGY) from non-phylogenetic similarity (ANALOGY). Here we extend the concept of phylogenetic homology by making a further distinction between a HOMOLOGOUS CHARACTER and a HOMOLOGOUS CHARACTER STATE. This distinction is important to molecular evolution, as we often deal with data comprised of homologous characters with non-homologous character states. The figure below shows three hypothetical protein-coding nucleotide sequences (for simplicity, only three codons long) that are related to each other according to a phylogenetic tree. In the figure the nucleotide sequences are aligned to each other; in so doing we are making the implicit assumption that the characters aligned vertically are homologous characters. In the specific case of nucleotide and amino acid alignments this assumption is called POSITIONAL HOMOLOGY. Under positional homology it is implicit that a given position, say the first position in the gene sequence, was the same in the gene sequence of the common ancestor. In the figure below it is clear that some positions do not have identical character states (see red characters in figure below). In such a case the involved position is considered to be a homologous character, while the state of that character will be non-homologous where there are differences. Phylogenetic perspective on homologous characters and homologous character states ACG TAC TAA SYNAPOMORPHY: a shared derived character state in C two or more lineages. ACG TAT TAA These must be homologous in state.
    [Show full text]
  • Phylogenetics of Buchnera Aphidicola Munson Et Al., 1991
    Türk. entomol. derg., 2019, 43 (2): 227-237 ISSN 1010-6960 DOI: http://dx.doi.org/10.16970/entoted.527118 E-ISSN 2536-491X Original article (Orijinal araştırma) Phylogenetics of Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae) based on 16S rRNA amplified from seven aphid species1 Farklı yaprak biti türlerinden izole edilen Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae)’nın 16S rRNA’ya göre filogenetiği Gül SATAR2* Abstract The obligate symbiont, Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae) is important for the physiological processes of aphids. Buchnera aphidicola genes detected in seven aphid species, collected in 2017 from different plants and altitudes in Adana Province, Turkey were analyzed to reveal phylogenetic interactions between Buchnera and aphids. The 16S rRNA gene was amplified and sequenced for this purpose and a phylogenetic tree built up by the neighbor-joining method. A significant correlation between B. aphidicola genes and the aphid species was revealed by this phylogenetic tree and the haplotype network. Specimens collected in Feke from Solanum melongena L. was distinguished from the other B. aphidicola genes on Aphis gossypii Glover, 1877 (Hemiptera: Aphididae) with a high bootstrap value of 99. Buchnera aphidicola in Myzus spp. was differentiated from others, and the difference between Myzus cerasi (Fabricius, 1775) and Myzus persicae (Sulzer, 1776) was clear. Although, B. aphidicola is specific to its host aphid, certain nucleotide differences obtained within the species could enable specification to geographic region or host plant in the future. Keywords: Aphid, genetic similarity, phylogenetics, symbiotic bacterium Öz Obligat simbiyont, Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae), yaprak bitlerinin fizyolojik olaylarının sürdürülmesinde önemli bir rol oynar.
    [Show full text]
  • Introductory Activities
    TEACHER’S GUIDE Introduction Dean Madden Introductory NCBE, University of Reading activities Version 1.0 CaseCase Studies introduction Introductory activities The activities in this section explain the basic principles behind the construction of phylogenetic trees, DNA structure and sequence alignment. Students are also intoduced to the Geneious software. Before carrying out the activities in the DNA to Darwin Case studies, students will need to understand: • the basic principles behind the construction of an evolutionary tree or phylogeny; • the basic structure of DNA and proteins; • the reasons for and the principle of alignment; • use of some features of the Geneious computer software (basic version). The activities in this introduction are designed to achieve this. Some of them will reinforce what students may already know; others involve new concepts. The material includes extension activities for more able students. Evolutionary trees In 1837, 12 years before the publication of On the Origin of Species, Charles Darwin famously drew an evolutionary tree in one of his notebooks. The Origin also included a diagram of an evolutionary tree — the only illustration in the book. Two years before, Darwin had written to his friend Thomas Henry Huxley, saying: ‘The time will come, I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of Nature.’ Today, scientists are trying to produce the ‘Tree of Life’ Darwin foresaw, using protein, DNA and RNA sequence data. Evolutionary trees are covered on pages 2–7 of the Student’s guide and in the PowerPoint and Keynote slide presentations.
    [Show full text]
  • Understanding Cladistics
    Understanding Cladistics Activity for Grades 5–8 Introduction Objective At the American Museum of Natural History, In this activity, students will explore cladistics and scientists use a method called cladistics to group create a cladogram of their own. animals. They look for unique features, such as a hole in the hip socket, that the animals share. Materials Animals with like features are grouped together. A • Understanding Cladistics chart, called a cladogram, shows these relationships. • A penny, nickel, dime, and quarter for each pair Using cladistics, scientists can reconstruct genealogi- of students cal relationships and can show how animals are • 6-8 dinosaurs pictures duplicated for each group, linked to one another through a long and complex downloadable from history of evolutionary changes. amnh.org/resources/rfl/pdf/dino_16_illustrations.pdf Procedure 1. Write lion, elephant, zebra, kangaroo, koala, buffalo, raccoon, and alligator. Ask students how the animals are related and what might be a good way of grouping them into sets and subsets. Discuss students responses. Tyrannosaurus rex Apatosaurus excelsus 2. Explain to students that scientists use a method extinct extinct called cladistics to determine evolutionary relation- ships among animals. They look for features that animals share, such as four limbs, hooves, or a hole in the hip socket. Animals with like features are grouped together. Scientists make a chart called a cladogram to show these relationships. 3. Tell students that they will examine the features of various coins to determine how they are related. Remind students that cladistics is used to determine relationships among organisms, and Theropoda Sauropoda Foot with three main At least 11 or more not necessarily objects.
    [Show full text]
  • Burmese Amber Taxa
    Burmese (Myanmar) amber taxa, on-line supplement v.2021.1 Andrew J. Ross 21/06/2021 Principal Curator of Palaeobiology Department of Natural Sciences National Museums Scotland Chambers St. Edinburgh EH1 1JF E-mail: [email protected] Dr Andrew Ross | National Museums Scotland (nms.ac.uk) This taxonomic list is a supplement to Ross (2021) and follows the same format. It includes taxa described or recorded from the beginning of January 2021 up to the end of May 2021, plus 3 species that were named in 2020 which were missed. Please note that only higher taxa that include new taxa or changed/corrected records are listed below. The list is until the end of May, however some papers published in June are listed in the ‘in press’ section at the end, but taxa from these are not yet included in the checklist. As per the previous on-line checklists, in the bibliography page numbers have been added (in blue) to those papers that were published on-line previously without page numbers. New additions or changes to the previously published list and supplements are marked in blue, corrections are marked in red. In Ross (2021) new species of spider from Wunderlich & Müller (2020) were listed as being authored by both authors because there was no indication next to the new name to indicate otherwise, however in the introduction it was indicated that the author of the new taxa was Wunderlich only. Where there have been subsequent taxonomic changes to any of these species the authorship has been corrected below.
    [Show full text]
  • Phylogeny Diversity: a Phylogenetic Framework Phenetics
    Speciation is a Phylogeny process by which lineages split. -the evolutionary relationships among We should be able organisms to the reconstruct the history of these (millions of Time years) -the patterns of lineage branching produced splits (i.e., build an by the true evolutionary history evolutionary tree) Linnaean System Diversity: of Classification A Phylogenetic Framework I. Taxonomy II. Phenetics III. Cladistics Carl von Linné a.k.a. Linnaeus (1707-1778) Phenetics Taxonomy does not always reflect evolutionary history. • Grouping is based on phenotypic similarity • Does not distinguish the cause of similarities • Not widely used today because many Example: Example: Example: similarities are not due to common ancestry. Class Aves Kingdom Protista Class Reptilia 1 Convergent Evolution Cladistics • Emphasizes common ancestry (≠ similarity) • Distinguishes between two kinds of similarities: 1) similarity due to common ancestry 2) similarity due to convergent evolution • Most widely used approach to reconstructing phylogenies. Homology Bird feathers are made of keratin. a phenotype that is similar in two species because it was inherited from a common ancestor. fly wings ≠ bird wings Homoplasy a phenotype that is similar in two species because of convergent evolution. Insect wings are made of chiton. An Example of Cladistics Relate the following taxa: • Horse • Seal • Lion • House Cat Homoplasy 2 Data for Cladistic Analysis How to do a Cladistic Analysis * * Cat Lion Horse Seal Cat Lion Horse 1. Define a set of traits. Seal Lizard Trait Lizard 2. Analyze traits for homology. Retractable Claws 1 0 0 0 0 Pointed Molars 1 1 0 0 0 3. Assign phenotypic states to each taxon.
    [Show full text]
  • 'The Realm of Hard Evidence': Novelty, Persuasion And
    Stud. Hist. Phil. Biol. & Biomed. Sci., Vol. 32, No. 2, pp. 343–360, 2001 Pergamon 2001 Elsevier Science Ltd. All rights reserved. Printed in Great Britain 1369-8486/01 $ - see front matter www.elsevier.com/locate/shpsc ‘The Realm of Hard Evidence’: Novelty, Persuasion and Collaboration in Botanical Cladistics Jim Endersby* In 1998 a new classification of flowering plants generated headlines in the non- specialist press in Britain. By interviewing those involved with, or critical of, the new classification, this essay examines the participants’ motives and strategies for creating and maintaining a research group. It argues that the classification was produced by an informal alliance whose members collaborated despite their disagreements. This collaboration was possible because standardised methods and common theoretical assumptions served as ‘boundary objects’. The group also created a novel form of collective publication that helped to unite them. Both the collaboration and the pub- lishing strategy were partly motivated by the need to give taxonomy a degree of ‘big science’ credibility that it had previously lacked: creating an international team allowed more comprehensive results; and collective publication served to emphasise both the novelty of the work and its claims to objectivity. Creating a group identity also served to exclude practitioners of alternative forms of taxonomy. Finally, the need to obtain funding for continuing work both created the need to collaborate and influenced the way the classification was presented to the public. 2001 Elsevier Science Ltd. All rights reserved. Keywords: Cladistics; Botanical Taxonomy; Boundary Objects; Sociology of Science; Rhetoric of Science. 1. Introduction: ‘A Rose is Still a Rose’ On 23rd November 1998, the Independent newspaper announced that ‘A rose is still a rose, but everything else in botany is turned on its head’.
    [Show full text]
  • Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity
    Acta Biotheor (2009) 57:129–162 DOI 10.1007/s10441-008-9064-7 REGULAR ARTICLE Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity Rasmus Grønfeldt Winther Received: 10 October 2008 / Accepted: 17 October 2008 / Published online: 7 January 2009 Ó Springer Science+Business Media B.V. 2009 Abstract The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free ‘‘view from nowhere.’’ Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. Keywords Characters Á Cladistics Á Phylogenetics Á Morphology Á Abstraction Á Reification Á Biological theory Á Epistemology Á Causation How are we to recognize the ‘‘true’’ characters of organisms rather than imposing upon them arbitrary divisions that obscure the very processes that we seek to understand? …No issue is of greater importance in the study of biology. –Lewontin 2001, p. xvii Are characters natural units or artifacts of observation and description? In both systematics and ecology, there is often a considerable gulf between observables and the units that play causal roles in our models.
    [Show full text]
  • A Comparative Phenetic and Cladistic Analysis of the Genus Holcaspis Chaudoir (Coleoptera: .Carabidae)
    Lincoln University Digital Thesis Copyright Statement The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). This thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: you will use the copy only for the purposes of research or private study you will recognise the author's right to be identified as the author of the thesis and due acknowledgement will be made to the author where appropriate you will obtain the author's permission before publishing any material from the thesis. A COMPARATIVE PHENETIC AND CLADISTIC ANALYSIS OF THE GENUS HOLCASPIS CHAUDOIR (COLEOPTERA: CARABIDAE) ********* A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Lincoln University by Yupa Hanboonsong ********* Lincoln University 1994 Abstract of a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. A comparative phenetic and cladistic analysis of the genus Holcaspis Chaudoir (Coleoptera: .Carabidae) by Yupa Hanboonsong The systematics of the endemic New Zealand carabid genus Holcaspis are investigated, using phenetic and cladistic methods, to construct phenetic and phylogenetic relationships. Three different character data sets: morphological, allozyme and random amplified polymorphic DNA (RAPD) based on the polymerase chain reaction (PCR), are used to estimate the relationships. Cladistic and morphometric analyses are undertaken on adult morphological characters. Twenty six external morphological characters, including male and female genitalia, are used for cladistic analysis. The results from the cladistic analysis are strongly congruent with previous publications. The morphometric analysis uses multivariate discriminant functions, with 18 morphometric variables, to derive a phenogram by clustering from Mahalanobis distances (D2) of the discrimination analysis using the unweighted pair-group method with arithmetical averages (UPGMA).
    [Show full text]
  • 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).
    [Show full text]