Parsimony, Synapomorphy, and Explanatory Power: a Reply to Duncan
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Lecture 2 Phylogenetics of Fishes 1. Phylogenetic Systematics 2
Lecture 2 Phylogenetics of Fishes 1. Phylogenetic systematics 2. General fish evolution 3. Molecular systematics & Genetic approaches Charles Darwin & Alfred Russel Wallace All species are related through common descent 1809 - 1882 1823 - 1913 Willi Hennig (1913 – 1976) • Hennig developed cladistical method to infer relatedness • Goal is to correctly group ancestors and all their descendants Cladistics (a.k.a Phylogenetic Systematics) Fundamental approach • divide characters into two groups • Apomorphies: more recently derived characteristics • Pleisomorhpies: more ancestral, primitive characteristics • Identify Synapomorphies (shared derived characteristics) • group clades by synapomorphies Cladistics (a.k.a Phylogenetic Systematics) eyes Synapomorphy of rockfish, gills bichir, and sharks? jaws bony skeleton swim bladder Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics) eyes Sympleisomorphy of gills rockfish, bichir, and sharks? jaws bony skeleton swim bladder Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics) eyes “Ancestral” and “derived” are gills relative to your focal group jaws bony skeleton swim bladder Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics) Monophyletic (aka clade): all taxa are descended from a common ancestor that is not the ancestor of any other group (every taxa descended from that ancestor is included) examples? Cladistics (a.k.a Phylogenetic Systematics) Paraphyletic: the group does not contain all species descended from the most recent common ancestor of its members examples? Cladistics (a.k.a Phylogenetic Systematics) Polyphyletic: taxa are descended from several ancestors that are also the ancestors of taxa classified into other groups examples? Problems with Traditional Cladistics Homoplasies • traits evolved due to convergence - keel: stabilizes tail at high speeds Problems with Traditional Cladistics Statistically inconsistent • can lend more support for the wrong answer Bernal et al. -
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. -
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. -
Exclusivity As the Key to Defining a Phylogenetic Species Concept
Biol Philos (2009) 24:473–486 DOI 10.1007/s10539-009-9151-4 When monophyly is not enough: exclusivity as the key to defining a phylogenetic species concept Joel D. Velasco Received: 29 November 2008 / Accepted: 6 January 2009 / Published online: 20 January 2009 Ó Springer Science+Business Media B.V. 2009 Abstract A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of ‘‘the’’ Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species con- cept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees. Keywords Genealogical exclusivity Á Monophyly Á Phylogenetic species concept Á Phylogeneticsystematics Á Species Introduction The species problem—how to sort organisms into various species—remains a central problem in biological taxonomy. Despite many bitter disagreements about these fundamental units, there is widespread agreement on how to delimit ‘‘higher’’ taxa (those that are more inclusive than species). -
Evaluating the Monophyly and Biogeography of Cryptantha (Boraginaceae)
Systematic Botany (2018), 43(1): pp. 53–76 © Copyright 2018 by the American Society of Plant Taxonomists DOI 10.1600/036364418X696978 Date of publication April 18, 2018 Evaluating the Monophyly and Biogeography of Cryptantha (Boraginaceae) Makenzie E. Mabry1,2 and Michael G. Simpson1 1Department of Biology, San Diego State University, San Diego, California 92182, U. S. A. 2Current address: Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, U. S. A. Authors for correspondence ([email protected]; [email protected]) Abstract—Cryptantha, an herbaceous plant genus of the Boraginaceae, subtribe Amsinckiinae, has an American amphitropical disjunct distri- bution, found in western North America and western South America, but not in the intervening tropics. In a previous study, Cryptantha was found to be polyphyletic and was split into five genera, including a weakly supported, potentially non-monophyletic Cryptantha s. s. In this and subsequent studies of the Amsinckiinae, interrelationships within Cryptantha were generally not strongly supported and sample size was generally low. Here we analyze a greatly increased sampling of Cryptantha taxa using high-throughput, genome skimming data, in which we obtained the complete ribosomal cistron, the nearly complete chloroplast genome, and twenty-three mitochondrial genes. Our analyses have allowed for inference of clades within this complex with strong support. The occurrence of a non-monophyletic Cryptantha is confirmed, with three major clades obtained, termed here the Johnstonella/Albidae clade, the Maritimae clade, and a large Cryptantha core clade, each strongly supported as monophyletic. From these phylogenomic analyses, we assess the classification, character evolution, and phylogeographic history that elucidates the current amphitropical distribution of the group. -
Interpreting Cladograms Notes
Interpreting Cladograms Notes INTERPRETING CLADOGRAMS BIG IDEA: PHYLOGENIES DEPICT ANCESTOR AND DESCENDENT RELATIONSHIPS AMONG ORGANISMS BASED ON HOMOLOGY THESE EVOLUTIONARY RELATIONSHIPS ARE REPRESENTED BY DIAGRAMS CALLED CLADOGRAMS (BRANCHING DIAGRAMS THAT ORGANIZE RELATIONSHIPS) What is a Cladogram ● A diagram which shows ● Is not an evolutionary ___________ among tree, ___________show organisms. how ancestors are related ● Lines branching off other to descendants or how lines. The lines can be much they have changed traced back to where they branch off. These branching off points represent a hypothetical ancestor. Parts of a Cladogram Reading Cladograms ● Read like a family tree: show ________of shared ancestry between lineages. • When an ancestral lineage______: speciation is indicated due to the “arrival” of some new trait. Each lineage has unique ____to itself alone and traits that are shared with other lineages. each lineage has _______that are unique to that lineage and ancestors that are shared with other lineages — common ancestors. Quick Question #1 ●What is a_________? ● A group that includes a common ancestor and all the descendants (living and extinct) of that ancestor. Reading Cladogram: Identifying Clades ● Using a cladogram, it is easy to tell if a group of lineages forms a clade. ● Imagine clipping a single branch off the phylogeny ● all of the organisms on that pruned branch make up a clade Quick Question #2 ● Looking at the image to the right: ● Is the green box a clade? ● The blue? ● The pink? ● The orange? Reading Cladograms: Clades ● Clades are nested within one another ● they form a nested hierarchy. ● A clade may include many thousands of species or just a few. -
Conceptual Issues in Phylogeny, Taxonomy, and Nomenclature
Contributions to Zoology, 66 (1) 3-41 (1996) SPB Academic Publishing bv, Amsterdam Conceptual issues in phylogeny, taxonomy, and nomenclature Alexandr P. Rasnitsyn Paleontological Institute, Russian Academy ofSciences, Profsoyuznaya Street 123, J17647 Moscow, Russia Keywords: Phylogeny, taxonomy, phenetics, cladistics, phylistics, principles of nomenclature, type concept, paleoentomology, Xyelidae (Vespida) Abstract On compare les trois approches taxonomiques principales développées jusqu’à présent, à savoir la phénétique, la cladis- tique et la phylistique (= systématique évolutionnaire). Ce Phylogenetic hypotheses are designed and tested (usually in dernier terme s’applique à une approche qui essaie de manière implicit form) on the basis ofa set ofpresumptions, that is, of à les traits fondamentaux de la taxonomic statements explicite représenter describing a certain order of things in nature. These traditionnelle en de leur et particulier son usage preuves ayant statements are to be accepted as such, no matter whatever source en même temps dans la similitude et dans les relations de evidence for them exists, but only in the absence ofreasonably parenté des taxons en question. L’approche phylistique pré- sound evidence pleading against them. A set ofthe most current sente certains avantages dans la recherche de réponses aux phylogenetic presumptions is discussed, and a factual example problèmes fondamentaux de la taxonomie. ofa practical realization of the approach is presented. L’auteur considère la nomenclature A is made of the three -
II. a Cladistic Analysis of Rbcl Sequences and Morphology
Systematic Botany (2003), 28(2): pp. 270±292 q Copyright 2003 by the American Society of Plant Taxonomists Phylogenetic Relationships in the Commelinaceae: II. A Cladistic Analysis of rbcL Sequences and Morphology TIMOTHY M. EVANS,1,3 KENNETH J. SYTSMA,1 ROBERT B. FADEN,2 and THOMAS J. GIVNISH1 1Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin 53706; 2Department of Systematic Biology-Botany, MRC 166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012; 3Present address, author for correspondence: Department of Biology, Hope College, 35 East 12th Street, Holland, Michigan 49423-9000 ([email protected]) Communicating Editor: John V. Freudenstein ABSTRACT. The chloroplast-encoded gene rbcL was sequenced in 30 genera of Commelinaceae to evaluate intergeneric relationships within the family. The Australian Cartonema was consistently placed as sister to the rest of the family. The Commelineae is monophyletic, while the monophyly of Tradescantieae is in question, due to the position of Palisota as sister to all other Tradescantieae plus Commelineae. The phylogeny supports the most recent classi®cation of the family with monophyletic tribes Tradescantieae (minus Palisota) and Commelineae, but is highly incongruent with a morphology-based phylogeny. This incongruence is attributed to convergent evolution of morphological characters associated with pollination strategies, especially those of the androecium and in¯orescence. Analysis of the combined data sets produced a phylogeny similar to the rbcL phylogeny. The combined analysis differed from the molecular one, however, in supporting the monophyly of Dichorisandrinae. The family appears to have arisen in the Old World, with one or possibly two movements to the New World in the Tradescantieae, and two (or possibly one) subsequent movements back to the Old World; the latter are required to account for the Old World distribution of Coleotrypinae and Cyanotinae, which are nested within a New World clade. -
Hemiplasy and Homoplasy in the Karyotypic Phylogenies of Mammals
Hemiplasy and homoplasy in the karyotypic phylogenies of mammals Terence J. Robinson*†, Aurora Ruiz-Herrera‡, and John C. Avise†§ *Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa; ‡Laboratorio di Biologia Cellulare e Molecolare, Dipartimento di Genetica e Microbiologia, Universita`degli Studi di Pavia, via Ferrata 1, 27100 Pavia, Italy; and §Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 Contributed by John C. Avise, July 31, 2008 (sent for review May 28, 2008) Phylogenetic reconstructions are often plagued by difficulties in (2). These syntenic blocks, sometimes shared across even dis- distinguishing phylogenetic signal (due to shared ancestry) from tantly related species, may involve entire chromosomes, chro- phylogenetic noise or homoplasy (due to character-state conver- mosomal arms, or chromosomal segments. Based on the premise gences or reversals). We use a new interpretive hypothesis, termed that each syntenic assemblage in extant species is of monophy- hemiplasy, to show how random lineage sorting might account for letic origin, researchers have reconstructed phylogenies and specific instances of seeming ‘‘phylogenetic discordance’’ among ancestral karyotypes for numerous mammalian taxa (ref. 3 and different chromosomal traits, or between karyotypic features and references therein). Normally, the phylogenetic inferences from probable species phylogenies. We posit that hemiplasy is generally these cladistic appraisals are self-consistent (across syntenic less likely for underdominant chromosomal polymorphisms (i.e., blocks) and taxonomically reasonable, and they have helped those with heterozygous disadvantage) than for neutral polymor- greatly to identify particular mammalian clades. However, in a phisms or especially for overdominant rearrangements (which few cases problematic phylogenetic patterns of the sort described should tend to be longer-lived), and we illustrate this concept by above have emerged. -
Phylogenetic Analysis
Phylogenetic Analysis Aristotle • Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus • Swedish botanist (1700s) • Listed all known species • Developed scheme of classification to discover the plan of the Creator 1 Linnaeus’ Main Contributions 1) Hierarchical classification scheme Kingdom: Phylum: Class: Order: Family: Genus: Species 2) Binomial nomenclature Before Linnaeus physalis amno ramosissime ramis angulosis glabris foliis dentoserratis After Linnaeus Physalis angulata (aka Cutleaf groundcherry) 3) Originated the practice of using the ♂ - (shield and arrow) Mars and ♀ - (hand mirror) Venus glyphs as the symbol for male and female. Charles Darwin • Species evolved from common ancestors. • Concept of closely related species being more recently diverged from a common ancestor. Therefore taxonomy might actually represent phylogeny! The phylogeny and classification of life a proposed by Haeckel (1866). 2 Trees - Rooted and Unrooted 3 Trees - Rooted and Unrooted ABCDEFGHIJ A BCDEH I J F G ROOT ROOT D E ROOT A F B H J G C I 4 Monophyletic: A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor. A monophyletic taxon is also called a clade. Paraphyletic: A group composed of a collection of organisms, including the most recent common ancestor of all those organisms. Unlike a monophyletic group, a paraphyletic group does not include all the descendants of the most recent common ancestor. Polyphyletic: A group composed of a collection of organisms in which the most recent common ancestor of all the included organisms is not included, usually because the common ancestor lacks the characteristics of the group. -
How to Build a Cladogram
Name: _____________________________________ TOC#____ How to Build a Cladogram. Background: Cladograms are diagrams that we use to show phylogenies. A phylogeny is a hypothesized evolutionary history between species that takes into account things such as physical traits, biochemical traits, and fossil records. To build a cladogram one must take into account all of these traits and compare them among organisms. Building a cladogram can seem challenging at first, but following a few simple steps can be very beneficial. Watch the following, short video, read the directions, and then practice building some cladograms. Video: http://ccl.northwestern.edu/simevolution/obonu/cladograms/Open-This-File.swf Instructions: There are two steps that will help you build a cladogram. Step One “The Chart”: 1. First, you need to make a “characteristics chart” the helps you analyze which characteristics each specieshas. Fill in a “x” for yes it has the trait and “o” for “no” for each of the organisms below. 2. Then you count how many times you wrote yes for each characteristic. Those characteristics with a large number of “yeses” are more ancestral characteristics because they are shared by many. Those traits with fewer yeses, are shared derived characters, or derived characters and have evolved later. Chart Example: Backbone Legs Hair Earthworm O O O Fish X O O Lizard X X O Human X X X “yes count” 3 2 1 Step Two “The Venn Diagram”: This step will help you to learn to build Cladograms, but once you figure it out, you may not always need to do this step.