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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. -
Foucault's Darwinian Genealogy
genealogy Article Foucault’s Darwinian Genealogy Marco Solinas Political Philosophy, University of Florence and Deutsches Institut Florenz, Via dei Pecori 1, 50123 Florence, Italy; [email protected] Academic Editor: Philip Kretsedemas Received: 10 March 2017; Accepted: 16 May 2017; Published: 23 May 2017 Abstract: This paper outlines Darwin’s theory of descent with modification in order to show that it is genealogical in a narrow sense, and that from this point of view, it can be understood as one of the basic models and sources—also indirectly via Nietzsche—of Foucault’s conception of genealogy. Therefore, this essay aims to overcome the impression of a strong opposition to Darwin that arises from Foucault’s critique of the “evolutionistic” research of “origin”—understood as Ursprung and not as Entstehung. By highlighting Darwin’s interpretation of the principles of extinction, divergence of character, and of the many complex contingencies and slight modifications in the becoming of species, this essay shows how his genealogical framework demonstrates an affinity, even if only partially, with Foucault’s genealogy. Keywords: Darwin; Foucault; genealogy; natural genealogies; teleology; evolution; extinction; origin; Entstehung; rudimentary organs “Our classifications will come to be, as far as they can be so made, genealogies; and will then truly give what may be called the plan of creation. The rules for classifying will no doubt become simpler when we have a definite object in view. We possess no pedigrees or armorial bearings; and we have to discover and trace the many diverging lines of descent in our natural genealogies, by characters of any kind which have long been inherited. -
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). -
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. -
Synthesis of Phylogeny and Taxonomy Into a Comprehensive Tree of Life
Synthesis of phylogeny and taxonomy into a comprehensive tree of life Cody E. Hinchliffa,1, Stephen A. Smitha,1,2, James F. Allmanb, J. Gordon Burleighc, Ruchi Chaudharyc, Lyndon M. Coghilld, Keith A. Crandalle, Jiabin Dengc, Bryan T. Drewf, Romina Gazisg, Karl Gudeh, David S. Hibbettg, Laura A. Katzi, H. Dail Laughinghouse IVi, Emily Jane McTavishj, Peter E. Midfordd, Christopher L. Owenc, Richard H. Reed, Jonathan A. Reesk, Douglas E. Soltisc,l, Tiffani Williamsm, and Karen A. Cranstonk,2 aEcology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109; bInterrobang Corporation, Wake Forest, NC 27587; cDepartment of Biology, University of Florida, Gainesville, FL 32611; dField Museum of Natural History, Chicago, IL 60605; eComputational Biology Institute, George Washington University, Ashburn, VA 20147; fDepartment of Biology, University of Nebraska-Kearney, Kearney, NE 68849; gDepartment of Biology, Clark University, Worcester, MA 01610; hSchool of Journalism, Michigan State University, East Lansing, MI 48824; iBiological Science, Clark Science Center, Smith College, Northampton, MA 01063; jDepartment of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045; kNational Evolutionary Synthesis Center, Duke University, Durham, NC 27705; lFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; and mComputer Science and Engineering, Texas A&M University, College Station, TX 77843 Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved July 28, 2015 (received for review December 3, 2014) Reconstructing the phylogenetic relationships that unite all line- published phylogenies are available only as journal figures, rather ages (the tree of life) is a grand challenge. The paucity of homologous than in electronic formats that can be integrated into databases and character data across disparately related lineages currently renders synthesis methods (7–9). -
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. -
Species Tree Likelihood Computation Given SNP Data Using Ancestral Configurations
Species Tree Likelihood Computation Given SNP Data Using Ancestral Configurations DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hang Fan, M.S. Graduate Program in Statistics The Ohio State University 2013 Dissertation Committee: Professor Laura Kubatko, Advisor Professor Bryan Carstens Professor Radu Herbei 1 Copyright by Hang Fan 2013 2 Abstract Inferring species trees given genetic data has been a challenge in the field of phylogenetics because of the high intensity during computation. In the coalescent framework, this dissertation proposes an innovative method of estimating the likelihood of a species tree directly from Single Nucleotide Polymorphism (SNP) data with a certain nucleotide substitution model. This method uses the idea of Ancestral Configurations (Wu, 2011) to avoid the computation burden brought by the enumeration of coalescent histories. Importance sampling is used to in Monte Carlo integration to approximate the expectations in the computation, where the accuracy of the approximation is tested in different tree models. The SNP data is processed beforehand which vastly boosts the efficiency of the method. Gene tree sampling given the species tree under the coalescent model is employed to make the computation feasible for large trees. Further, the branch lengths on the species tree are optimized according to the computed species tree likelihood, which provides the likelihood of the species tree topology given the SNP data. For inference, this likelihood computation method is implemented in the stepwise addition algorithm to infer the maximum likelihood species tree in the tree space given the SNP data, and simulations are conduced to test the performance. -
EVOLUTIONARY INFERENCE: Some Basics of Phylogenetic Analyses
EVOLUTIONARY INFERENCE: Some basics of phylogenetic analyses. Ana Rojas Mendoza CNIO-Madrid-Spain. Alfonso Valencia’s lab. Aims of this talk: • 1.To introduce relevant concepts of evolution to practice phylogenetic inference from molecular data. • 2.To introduce some of the most useful methods and computer programmes to practice phylogenetic inference. • • 3.To show some examples I’ve worked in. SOME BASICS 11--ConceptsConcepts ofof MolecularMolecular EvolutionEvolution • Homology vs Analogy. • Homology vs similarity. • Ortologous vs Paralogous genes. • Species tree vs genes tree. • Molecular clock. • Allele mutation vs allele substitution. • Rates of allele substitution. • Neutral theory of evolution. SOME BASICS Owen’s definition of homology Richard Owen, 1843 • Homologue: the same organ under every variety of form and function (true or essential correspondence). •Analogy: superficial or misleading similarity. SOME BASICS 1.Concepts1.Concepts ofof MolecularMolecular EvolutionEvolution • Homology vs Analogy. • Homology vs similarity. • Ortologous vs Paralogous genes. • Species tree vs genes tree. • Molecular clock. • Allele mutation vs allele substitution. • Rates of allele substitution. • Neutral theory of evolution. SOME BASICS Similarity ≠ Homology • Similarity: mathematical concept . Homology: biological concept Common Ancestry!!! SOME BASICS 1.Concepts1.Concepts ofof MolecularMolecular EvolutionEvolution • Homology vs Analogy. • Homology vs similarity. • Ortologous vs Paralogous genes. • Species tree vs genes tree. • Molecular clock. -
The Probability of Monophyly of a Sample of Gene Lineages on a Species Tree
PAPER The probability of monophyly of a sample of gene COLLOQUIUM lineages on a species tree Rohan S. Mehtaa,1, David Bryantb, and Noah A. Rosenberga aDepartment of Biology, Stanford University, Stanford, CA 94305; and bDepartment of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand Edited by John C. Avise, University of California, Irvine, CA, and approved April 18, 2016 (received for review February 5, 2016) Monophyletic groups—groups that consist of all of the descendants loci that are reciprocally monophyletic is informative about the of a most recent common ancestor—arise naturally as a conse- time since species divergence and can assist in representing the quence of descent processes that result in meaningful distinctions level of differentiation between groups (4, 18). between organisms. Aspects of monophyly are therefore central to Many empirical investigations of genealogical phenomena have fields that examine and use genealogical descent. In particular, stud- made use of conceptual and statistical properties of monophyly ies in conservation genetics, phylogeography, population genetics, (19). Comparisons of observed monophyly levels to model pre- species delimitation, and systematics can all make use of mathemat- dictions have been used to provide information about species di- ical predictions under evolutionary models about features of mono- vergence times (20, 21). Model-based monophyly computations phyly. One important calculation, the probability that a set of gene have been used alongside DNA sequence differences between and lineages is monophyletic under a two-species neutral coalescent within proposed clades to argue for the existence of the clades model, has been used in many studies. Here, we extend this calcu- (22), and tests involving reciprocal monophyly have been used to lation for a species tree model that contains arbitrarily many species. -
Ten Misunderstandings About Evolution a Very Brief Guide for the Curious and the Confused by Dr
Ten Misunderstandings About Evolution A Very Brief Guide for the Curious and the Confused By Dr. Mike Webster, Dept. of Neurobiology and Behavior, Cornell Lab of Ornithology, Cornell University ([email protected]); February 2010 The current debate over evolution and “intelligent design” (ID) is being driven by a relatively small group of individuals who object to the theory of evolution for religious reasons. The debate is fueled, though, by misunderstandings on the part of the American public about what evolutionary biology is and what it says. These misunderstandings are exploited by proponents of ID, intentionally or not, and are often echoed in the media. In this booklet I briefly outline and explain 10 of the most common (and serious) misunderstandings. It is impossible to treat each point thoroughly in this limited space; I encourage you to read further on these topics and also by visiting the websites given on the resource sheet. In addition, I am happy to send a somewhat expanded version of this booklet to anybody who is interested – just send me an email to ask for one! What are the misunderstandings? 1. Evolution is progressive improvement of species Evolution, particularly human evolution, is often pictured in textbooks as a string of organisms marching in single file from “simple” organisms (usually a single celled organism or a monkey) on one side of the page and advancing to “complex” organisms on the opposite side of the page (almost invariably a human being). We have all seen this enduring image and likely have some version of it burned into our brains. -
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. -
Darwin's “Tree of Life”
Icons of Evolution? Why Much of What Jonathan Wells Writes about Evolution is Wrong Alan D. Gishlick, National Center for Science Education DARWIN’S “TREE OF LIFE” mon descent. Finally, he demands that text- books treat universal common ancestry as PHYLOGENETIC TREES unproven and refrain from illustrating that n biology, a phylogenetic tree, or phyloge- “theory” with misleading phylogenies. ny, is used to show the genealogic relation- Therefore, according to Wells, textbooks Iships of living things. A phylogeny is not should state that there is no evidence for com- so much evidence for evolution as much as it mon descent and that the most recent research is a codification of data about evolutionary his- refutes the concept entirely. Wells is complete- tory. According to biological evolution, organ- ly wrong on all counts, and his argument is isms share common ancestors; a phylogeny entirely based on misdirection and confusion. shows how organisms are related. The tree of He mixes up these various topics in order to life shows the path evolution took to get to the confuse the reader into thinking that when current diversity of life. It also shows that we combined, they show an endemic failure of can ascertain the genealogy of disparate living evolutionary theory. In effect, Wells plays the organisms. This is evidence for evolution only equivalent of an intellectual shell game, put- in that we can construct such trees at all. If ting so many topics into play that the “ball” of evolution had not happened or common ances- evolution gets lost. try were false, we would not be able to discov- THE CAMBRIAN EXPLOSION er hierarchical branching genealogies for ells claims that the Cambrian organisms (although textbooks do not general- Explosion “presents a serious chal- ly explain this well).