DOCSLIB.ORG

Understanding Phylogenetic Trees

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Understanding Phylogenetic Trees Today’s lecture Understanding phylogenetic trees What is phylogeny? Phylogeny = the pattern of evolutionary relationships among species, their descent from common ancestors “… the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications.” Charles Darwin, On the Origin of Species (1859) Augustin Augier, 1801 Heinrich Bronn, 1858 Haeckel, 1866 Haeckel, 1874 What is phylogeny? Phylogeny is often presented as a diagram (a phylogenetic tree). 1. Haeckel, 1866 2. Wikipedia 3 3. APweb 4. Gomez, 2010 5. Cameron, 2000 4 1 5 2 Interpreting phylogenetic trees Ingroup Outgroup Group 2 Group 1 H G F E D C B A Tip = extant species Terminal branch Node Internal branch (internode) = ancestral species Root = common ancestor time Ingroup = the lineage under consideration. Outgroup = a lineage that is not part of the ingroup. Sister group = the lineage that is most closely related to the lineage under consideration. Interpreting phylogenetic trees Topology = the branching pattern of a phylogenetic tree Sister relationships are reciprocal; sister groups are each other’s closest relatives (share a more recent common ancestor with each other than with any other group). Interpreting phylogenetic trees H G F E D C B A Monophyletic group (or clade) = a single lineage; a group composed of a common ancestor and all of its descendants. mono = one, phylum = tribe Interpreting phylogenetic trees H G F E D C B A Paraphyletic group = a group containing a common ancestor and some, but not all, of its descendants. para = near, not quite, phylum = tribe Interpreting phylogenetic trees H G F E D C B A Polyphyletic group = multiple lineages; a group that does not contain the common ancestor of its members. poly = many, phylum = tribe Phylogenetic classification Phylogenetic classification = a hierarchical ordering of taxa, according to phylogenetic relationships. The use of phylogeny to produce the classification. Often referred to as cladistics. Our goal is to recognize and name only monophyletic groups, to achieve nested sets that are hierarchically organized. Chordates Amniotes Mammals Phylogenetic classification HomeothermiaHomeothermia (animals: thatan example are “warm of blooded”):a polyphyletic mammals group and birds evolution.berkeley.edu Phylogenetic classification Reptiles: flightlessReptiles, animals dinosaurs: with keratin examples scales Birdsof paraphyletic: flying animals groups with keratin feathers biology.unm.edu Phylogenetic classification Why no polyphyletic groups? – Natural classification should reflect evolutionary relationship Why no paraphyletic groups? – Taxa at same rank should not contain one another – All members of a group should have their closest relative also belong to that group Recognizing monophyletic groups allows greater predictive power xkcd.com( Taxonomic revision Gadek et al., 2000 Alaska yellow cedar Before: Chamaecyparis nootkatensis Xanthocyparis vietnamensis Taxonomic revision Farjon et al., 2002 Alaska yellow cedar Before: Chamaecyparis nootkatensis Now: Xanthocyparis nootkatensis Taxonomic revision tomato Before: Lycopersicon esculentum Now: Solanum lycopersicum Spooner et al., 1993 Reconstructing phylogeny Phylogenetic inference = the process by which the branching pattern of evolutionary relationship (phylogeny) is estimated. A phylogenetic tree is a hypothesis; it is subject to re- evaluation upon the discovery of new evidence. How do we infer phylogeny? Reconstructing phylogeny From comparable similarities (characters); shared traits between species. The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical.Charles Darwin, On the Origin of Species (1859) Character/trait = a variable characteristic of an Charles Darwin photo by Leonard organism, or group of organisms. Darwin, 1874. From Woodall, 1884: Transactions of the Shropshire Archaeological Society Eg. Body covering; flower color Character states = the different forms a character can take. white yellow scales feathers Reconstructing phylogeny: characters Dial, 1992 Homology = homologous characters are those inherited from a common ancestor. The states of homologous characters are comparable with one another, and may provide insight into evolutionary relationship. Analogy = analogous characters have multiple, independent evolutionary origins. Analogous characters do not provide useful indicators of evolutionary relationship. Reconstructing phylogeny: characters Synapomorphy = shared, derived character. (from Greek: syn—together (shared) + apo—away + morph—form) A derived state shared by two or more lineages, which was present in their common ancestor, and is not found in other organisms. Synapomorphies diagnose monophyletic groups. E.g., angiosperms (flowering plants) Reconstructing phylogeny: characters Ovules enclosed in carpels: synapomorphy defining angiosperms Ovules enclosed in carpels Soltis et al., 2011 Reconstructing phylogeny: characters Symplesiomorphy = shared, ancestral character. (from Greek: syn—together (shared) + plesio—near + morph—form) An ancestral state shared by two or more lineages, which was present in their common ancestor, but is not found in all of its descendants. Symplesiomorphies diagnose paraphyletic groups. E.g., “dicots” vs. monocots Reconstructing phylogeny: characters Two seed leaves: symplesiomorphy defining “dicots” One seed leaf Reconstructing phylogeny: characters Homoplasy = convergent character, analogy. (from Greek: homo—same + plassein—to mold) A state shared by two or more lineages which is not due to common ancestry. Convergent evolution, or parallelism. Convergent characters diagnose polyphyletic groups. E.g., “Amentiferae” Reconstructing phylogeny: characters Wind pollination: multiple origins convergent characters associated with wind pollination, defining “Amentiferae” Reconstructing phylogeny: characters Polarity = direction of evolutionary change. Outgroup comparison Character states in the outgroup = ancestral condition in the ingroup. petals unfused = ancestral The preferred outgroup for determining polarity is the closest lineage to the ingroup: the sister group. Reconstructing phylogeny: in practice Parsimony = the principle that the best explanation is the simplest one. Trait a Trait b Trait c Taxon 1 Absent (0) Present (1) Absent (0) Taxon 2 Present (1) Absent (0) Present (1) Taxon 3 Present (1) Present (1) Present (1) Outgroup Absent (0) Absent (0) Absent (0) out 1 2 3 out 1 3 2 out 1 2 3 c b c b a c a c b c a a a b b 4 steps 5 steps 6 steps Reconstructing phylogeny: in practice In practice: many taxa, many characters; computationally intensive Felsenstein,(1978( Reconstructing phylogeny: in practice Real example with DNA sequence data (nucleotide characters). .
Load more

Recommended publications
  • 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.
    [Show full text]
  • Untangling Phylogenetic Patterns and Taxonomic Confusion in Tribe Caryophylleae (Caryophyllaceae) with Special Focus on Generic
    TAXON 67 (1) • February 2018: 83–112 Madhani & al. • Phylogeny and taxonomy of Caryophylleae (Caryophyllaceae) Untangling phylogenetic patterns and taxonomic confusion in tribe Caryophylleae (Caryophyllaceae) with special focus on generic boundaries Hossein Madhani,1 Richard Rabeler,2 Atefeh Pirani,3 Bengt Oxelman,4 Guenther Heubl5 & Shahin Zarre1 1 Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran 2 University of Michigan Herbarium-EEB, 3600 Varsity Drive, Ann Arbor, Michigan 48108-2228, U.S.A. 3 Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, P.O. Box 91775-1436, Mashhad, Iran 4 Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Göteborg, Sweden 5 Biodiversity Research – Systematic Botany, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany; and GeoBio Center LMU Author for correspondence: Shahin Zarre, [email protected] DOI https://doi.org/10.12705/671.6 Abstract Assigning correct names to taxa is a challenging goal in the taxonomy of many groups within the Caryophyllaceae. This challenge is most serious in tribe Caryophylleae since the supposed genera seem to be highly artificial, and the available morphological evidence cannot effectively be used for delimitation and exact determination of taxa. The main goal of the present study was to re-assess the monophyly of the genera currently recognized in this tribe using molecular phylogenetic data. We used the sequences of nuclear ribosomal internal transcribed spacer (ITS) and the chloroplast gene rps16 for 135 and 94 accessions, respectively, representing all 16 genera currently recognized in the tribe Caryophylleae, with a rich sampling of Gypsophila as one of the most heterogeneous groups in the tribe.
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]
  • Genomic Analysis of the Tribe Emesidini (Lepidoptera: Riodinidae)
    Zootaxa 4668 (4): 475–488 ISSN 1175-5326 (print edition) https://www.mapress.com/j/zt/ Article ZOOTAXA Copyright © 2019 Magnolia Press ISSN 1175-5334 (online edition) https://doi.org/10.11646/zootaxa.4668.4.2 http://zoobank.org/urn:lsid:zoobank.org:pub:211AFB6A-8C0A-4AB2-8CF6-981E12C24934 Genomic analysis of the tribe Emesidini (Lepidoptera: Riodinidae) JING ZHANG1, JINHUI SHEN1, QIAN CONG1,2 & NICK V. GRISHIN1,3 1Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, and 3Howard Hughes Medical Insti- tute, 5323 Harry Hines Blvd, Dallas, TX, USA 75390-9050; [email protected] 2present address: Institute for Protein Design and Department of Biochemistry, University of Washington, 1959 NE Pacific Street, HSB J-405, Seattle, WA, USA 98195; [email protected] Abstract We obtained and phylogenetically analyzed whole genome shotgun sequences of nearly all species from the tribe Emesidini Seraphim, Freitas & Kaminski, 2018 (Riodinidae) and representatives from other Riodinidae tribes. We see that the recently proposed genera Neoapodemia Trujano, 2018 and Plesioarida Trujano & García, 2018 are closely allied with Apodemia C. & R. Felder, [1865] and are better viewed as its subgenera, new status. Overall, Emesis Fabricius, 1807 and Apodemia (even after inclusion of the two subgenera) are so phylogenetically close that several species have been previously swapped between these two genera. New combinations are: Apodemia (Neoapodemia) zela (Butler, 1870), Apodemia (Neoapodemia) ares (Edwards, 1882), and Apodemia (Neoapodemia) arnacis (Stichel, 1928) (not Emesis); and Emesis phyciodoides (Barnes & Benjamin, 1924) (not Apodemia), assigned to each genus by their monophyly in genomic trees with the type species (TS) of the genus.
    [Show full text]
  • Statistical Inference for the Linguistic and Non-Linguistic Past
    Statistical inference for the linguistic and non-linguistic past Igor Yanovich DFG Center for Advanced Study “Words, Bones, Genes and Tools” Universität Tübingen July 6, 2017 Igor Yanovich 1 / 46 Overview of the course Overview of the course 1 Today: trees, as a description and as a process 2 Classes 2-3: simple inference of language-family trees 3 Classes 4-5: computational statistical inference of trees and evolutionary parameters 4 Class 6: histories of languages and of genes 5 Class 7: simple spatial statistics 6 Class 8: regression taking into account linguistic relationships; synthesis of the course Igor Yanovich 2 / 46 Overview of the course Learning outcomes By the end of the course, you should be able to: 1 read and engage with the current literature in linguistic phylogenetics and in spatial statistics for linguistics 2 run phylogenetic and basic spatial analyses on linguistic data 3 proceed further in the subject matter on your own, towards further advances in the field Igor Yanovich 3 / 46 Overview of the course Today’s class 1 Overview of the course 2 Language families and their structures 3 Trees as classifications and as process depictions 4 Linguistic phylogenetics 5 Worries about phylogenetics in linguistics vs. biology 6 Quick overview of the homework 7 Summary of Class 1 Igor Yanovich 4 / 46 Language families and their structures Language families and their structures Igor Yanovich 5 / 46 Language families and their structures Dravidian A modification of [Krishnamurti, 2003, Map 1.1], from Wikipedia Igor Yanovich 6 / 46 Language families and their structures Dravidian [Krishnamurti, 2003]’s classification: Dravidian family South Dravidian Central Dravidian North Dravidian SD I SD II Tamil Malay¯al.am Kannad.a Telugu Kolami Brahui (70M) (38M) (40M) (75M) (0.1M) (4M) (Numbers of speakers from Wikipedia) Igor Yanovich 7 / 46 Language families and their structures Dravidian: similarities and differences Proto-Dr.
    [Show full text]
  • H. Thorsten Lumbsch VP, Science & Education the Field Museum 1400
    H. Thorsten Lumbsch VP, Science & Education The Field Museum 1400 S. Lake Shore Drive Chicago, Illinois 60605 USA Tel: 1-312-665-7881 E-mail: [email protected] Research interests Evolution and Systematics of Fungi Biogeography and Diversification Rates of Fungi Species delimitation Diversity of lichen-forming fungi Professional Experience Since 2017 Vice President, Science & Education, The Field Museum, Chicago. USA 2014-2017 Director, Integrative Research Center, Science & Education, The Field Museum, Chicago, USA. Since 2014 Curator, Integrative Research Center, Science & Education, The Field Museum, Chicago, USA. 2013-2014 Associate Director, Integrative Research Center, Science & Education, The Field Museum, Chicago, USA. 2009-2013 Chair, Dept. of Botany, The Field Museum, Chicago, USA. Since 2011 MacArthur Associate Curator, Dept. of Botany, The Field Museum, Chicago, USA. 2006-2014 Associate Curator, Dept. of Botany, The Field Museum, Chicago, USA. 2005-2009 Head of Cryptogams, Dept. of Botany, The Field Museum, Chicago, USA. Since 2004 Member, Committee on Evolutionary Biology, University of Chicago. Courses: BIOS 430 Evolution (UIC), BIOS 23410 Complex Interactions: Coevolution, Parasites, Mutualists, and Cheaters (U of C) Reading group: Phylogenetic methods. 2003-2006 Assistant Curator, Dept. of Botany, The Field Museum, Chicago, USA. 1998-2003 Privatdozent (Assistant Professor), Botanical Institute, University – GHS - Essen. Lectures: General Botany, Evolution of lower plants, Photosynthesis, Courses: Cryptogams, Biology
    [Show full text]
  • 1 Integrative Biology 200 "PRINCIPLES OF
    Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler March 14, 2018. Classification II: Phylogenetic taxonomy including incorporation of fossils; PhyloCode I. Phylogenetic Taxonomy - the argument for rank-free classification A number of recent calls have been made for the reformation of the Linnaean hierarchy (e.g., De Queiroz & Gauthier, 1992). These authors have emphasized that the existing system is based in a non-evolutionary world-view; the roots of the Linnaean hierarchy are in a specially- created world-view. Perhaps the idea of fixed, comparable ranks made some sense under that view, but under an evolutionary world view they don't make sense. There are several problems with the current nomenclatorial system: 1. The current system, with its single type for a name, cannot be used to precisely name a clade. E.g., you may name a family based on a certain type specimen, and even if you were clear about what node you meant to name in your original publication, the exact phylogenetic application of your name would not be clear subsequently, after new clades are added. 2. There are not nearly enough ranks to name the thousands of levels of monophyletic groups in the tree of life. Therefore people are increasingly using informal rank-free names for higher- level nodes, but without any clear, formal specification of what clade is meant. 3. Most aspects of the current code, including priority, revolve around the ranks, which leads to instability of usage. For example, when a change in relationships is discovered, several names often need to be changed to adjust, including those of groups whose circumscription has not changed.
    [Show full text]
  • The Brilliant Tribe How to Avoid Burnout by Building a Tribe
    thethe good good life life | |ask adventure nisha THE BRILLIANT TRIBE HOW TO AVOID BURNOUT BY BUILDING A TRIBE NISHA JACKSON he body’s sophisticated response to stress is nothing short of » An encouraging community that allows you to make your passion a miracle. The reality, however, is that we overachiever-super- your livelihood. people-stress-junkies spend quite a bit of time being plugged Tin and in fight-or-flight mode, maneuvering strategically between one » Feeling like the luckiest person in the world in being surrounded by highly pressurized situation to the next. It’s like a time bomb. While those who care about you and have your back. our bodies are meant to react to perceived stress occasionally, they are clearly not capable of withstanding longer periods of flight or fight » And perhaps the greatest — and most unexpected — gift is that without some sort of breakdown. leading a community will serve as a catalyst for you to become a better human being. This elaborate stress response, with multiple internal alarms going off, typically occurs regularly throughout the day for most women. This 1. Start with a clear intention and a desire to have the group constant state of activation and overstimulation requires continuous you want. Consider listening to women or men talk and see effort to preserve and restore your adrenal glands. This is incredibly how you feel in their presence. For example, do you feel up, taxing on them, and causes your entire system to become sluggish. supported, enlightened, or engaged? Can you see this person Most people have heard of the fight or flight response.
    [Show full text]
  • Bioinfo 11 Phylogenetictree
    BIO 390/CSCI 390/MATH 390 Bioinformatics II Programming Lecture 11 Phylogenetic Tree Instructor: Lei Qian Fisk University Phylogenetic Tree Applications • Study ancestor-descendant relationships (Evolutionary biology, adaption, genetic drift, selection, speciation, etc.) • Paleogenomics: inferring ancestral genomic information from extinct species (Comparing Chimpanzee, Neanderthal and Human DNA) • Origins of epidemics (Comparing, at the molecular level, various virus strains) • Drug design: specially targeting groups of organisms (Efficient enumeration of phylogenetically informative substrings) • Forensic (Relationships among HIV strains) • Linguistics (Languages tree divergence times) Phylogenetic Tree Illustrating success stories in phylogenetics (I) For roughly 100 years (more exactly, 1870-1985), scientists were unable to figure out which family the giant panda belongs to. Giant pandas look like bears, but have features that are unusual for bears but typical to raccoons: they do not hibernate, they do not roar, their male genitalia are small and backward-pointing. Anatomical features were the dominant criteria used to derive evolutionary relationships between species since Darwin till early 1960s. The evolutionary relationships derived from these relatively subjective observations were often inconclusive. Some of them were later proved incorrect. In 1985, Steven O’Brien and colleagues solved the giant panda classification problem using DNA sequences and phylogenetic algorithms. Phylogenetic Tree Phylogenetic Tree Illustrating success stories in phylogenetics (II) In 1994, a woman from Lafayette, Louisiana (USA), clamed that her ex-lover (who was a physician) injected her with HIV+ blood. Records showed that the physician had drawn blood from a HIV+ patient that day. But how to prove that the blood from that HIV+ patient ended up in the woman? Phylogenetic Tree HIV has a high mutation rate, which can be used to trace paths of transmission.
    [Show full text]
  • Learning the “Game” of Life: Reconstruction of Cell Lineages Through Crispr-Induced Dna Mutations
    LEARNING THE “GAME” OF LIFE: RECONSTRUCTION OF CELL LINEAGES THROUGH CRISPR-INDUCED DNA MUTATIONS JIAXIAO CAI, DA KUANG, ARUN KIRUBARAJAN, MUKUND VENKATESWARAN ABSTRACT. Multi-cellular organisms are composed of many billions of individuals cells that exist by the mutation of a single stem cell. The CRISPR-based molecular-tools induce DNA mutations, which allows us to study the mutation lineages of various multi-ceulluar organisms. However, to date no lineage reconstruction algorithms have been examined for their performance/robustness across various molecular tools, datasets and sizes of lineage trees. In addition, it is unclear whether classical machine learning algorithms, deep neural networks or some combination of the two are the best approach for this task. In this paper, we introduce 1) a simulation framework for the zygote development process to achieve a dataset size required by deep learning models, and 2) various supervised and unsupervised approaches for cell mutation tree reconstruction. In particular, we show how deep generative models (Autoencoders and Variational Autoencoders), unsupervised clustering methods (K-means), and classical tree reconstruction algorithms (UPGMA) can all be used to trace cell mutation lineages. 1. INTRODUCTION Multi-cellular organisms are composed of billions or trillions of different interconnected cells that derive from a single cell through repeated rounds of cell division — knowing the cell lineage that produces a fully developed organism from a single cell provides the framework for understanding when, where, and how cell fate decisions are made. The recent advent of new CRISPR-based molecular tools synthetically induced DNA mutations and made it possible to solve lineage of complex model organisms at single-cell resolution.[1] Starting in early embryogenesis, CRISPR-induced mutations occur stochastically at introduced target sites, and these mutations are stably inherited by the offspring of these cells and immune to further change.
    [Show full text]