Seriation and Cladistics: the Difference Between Anagenetic and Cladogenetic Evolution
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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
Part II Specialized Studies Chapter Vi
Part II Specialized Studies chapter vi New Sites and Lingering Questions at the Debert and Belmont Sites, Nova Scotia Leah Morine Rosenmeier, Scott Buchanan, Ralph Stea, and Gordon Brewster ore than forty years ago the Debert site exca- presents a model for the depositional history of the site vations signaled a new standard for interdisci- area, including two divergent scenarios for the origins of the Mplinary approaches to the investigation of late cultural materials at the sites. We believe the expanded areal Pleistocene archaeological sites. The resulting excavations extent of the complex, the nature of past excavations, and produced a record that continues to anchor northeastern the degree of site preservation place the Debert- Belmont Paleoindian sites (MacDonald 1968). The Confederacy of complex among the largest, best- documented, and most Mainland Mi’kmaq (the Confederacy) has been increasingly intact Paleoindian sites in North America. involved with the protection and management of the site The new fi nds and recent research have resolved some complex since the discovery of the Belmont I and II sites in long- standing issues, but they have also created new debates. the late 1980s (Bernard et al. 2011; Julien et al. 2008). The Understanding the relative chronologies of the numerous data reported here are the result of archaeological testing site areas and the consequent relationship among the sites associated with these protection eff orts, the development of requires not only understanding depositional contexts for the Mi’kmawey Debert Cultural Centre (MDCC), and the single occupations but tying together varied contexts (rede- passage of new provincial regulations solely dedicated to pro- posited, disturbed, glaciofl uvial, glaciolacustrine, Holocene tecting archaeological sites in the Debert and Belmont area. -
Taxon Ordering in Phylogenetic Trees by Means of Evolutionary Algorithms Francesco Cerutti1,2, Luigi Bertolotti1,2, Tony L Goldberg3 and Mario Giacobini1,2*
Cerutti et al. BioData Mining 2011, 4:20 http://www.biodatamining.org/content/4/1/20 BioData Mining RESEARCH Open Access Taxon ordering in phylogenetic trees by means of evolutionary algorithms Francesco Cerutti1,2, Luigi Bertolotti1,2, Tony L Goldberg3 and Mario Giacobini1,2* * Correspondence: mario. Abstract [email protected] 1 Department of Animal Production, Background: In in a typical “left-to-right” phylogenetic tree, the vertical order of taxa Epidemiology and Ecology, Faculty of Veterinary Medicine, University is meaningless, as only the branch path between them reflects their degree of of Torino, Via Leonardo da Vinci similarity. To make unresolved trees more informative, here we propose an 44, 10095, Grugliasco (TO), Italy innovative Evolutionary Algorithm (EA) method to search the best graphical Full list of author information is available at the end of the article representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa. Methods: Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (l + μ)-EAs to study the influence of population on the algorithm. Results: The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (l + μ)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000). -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
A General Criterion for Translating Phylogenetic Trees Into Linear Sequences
A general criterion for translating phylogenetic trees into linear sequences Proposal (474) to South American Classification Committee In most of the books, papers and check-lists of birds (e.g. Meyer de Schauensee 1970, Stotz et al. 1996; and other taxa e.g. Lewis et al. 2005, Haston et al. 2009, for plants), at least the higher taxa are arranged phylogenetically, with the “oldest” groups (Rheiformes/Tinamiformes) placed first, and the “modern” birds (Passeriformes) at the end. The molecular phylogenetic analysis of Hackett et al. (2008) supports this criterion. For this reason, it would be desirable that in the SACC list not only orders and families, but also genera within families and species within genera, are phylogenetically ordered. In spite of the SACC’s efforts in producing an updated phylogeny-based list, it is evident that there are differences in the way the phylogenetic information has been translated into linear sequences, mainly for node rotation and polytomies. This is probably one of the reasons why Douglas Stotz (Proposal #423) has criticized using sequence to show relationships. He considers that we are creating unstable sequences with little value in terms of understanding of relationships. He added, “We would be much better served by doing what most taxonomic groups do and placing taxa within the hierarchy in alphabetical order, making no pretense that sequence can provide useful information on the branching patterns of trees. This would greatly stabilize sequences and not cost much information about relationships”. However, we encourage creating sequences that reflect phylogeny as much as possible at all taxonomic levels (although we agree with Douglas Stotz that the translation of a phylogenetic tree into a simple linear sequence inevitably involves a loss of information about relationships that is present in the trees on which the sequence is based). -
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. -
Genetic Change and Rates of Cladogenesis
GENETIC CHANGE AND RATES OF CLADOGENESIS JOHN C. AVISE* AND FRANCISCO J. AYALA Depariment of Genetics, University of Californiu, Davis, California 95616 Manuscript received May 12, 1975 Revised copy received July 28, 1975 ABSTRACT Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predic- tions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic dis- tance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. -
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. -
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography of Rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus)
City University of New York (CUNY) CUNY Academic Works Publications and Research New York City College of Technology 2016 Diversity-dependent cladogenesis throughout western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) Christopher Blair CUNY New York City College of Technology Santiago Sánchez-Ramírez University of Toronto How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/ny_pubs/344 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] 1Blair, C., Sánchez-Ramírez, S., 2016. Diversity-dependent cladogenesis throughout 2 western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: 3 Crotalus and Sistrurus ). Molecular Phylogenetics and Evolution 97, 145–154. 4 https://doi.org/10.1016/j.ympev.2015.12.020. © 2016. This manuscript version is made 5 available under the CC-BY-NC-ND 4.0 license. 6 7 8 Diversity-dependent cladogenesis throughout western Mexico: evolutionary 9 biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) 10 11 12 CHRISTOPHER BLAIR1*, SANTIAGO SÁNCHEZ-RAMÍREZ2,3,4 13 14 15 1Department of Biological Sciences, New York City College of Technology, Biology PhD 16 Program, Graduate Center, The City University of New York, 300 Jay Street, Brooklyn, 17 NY 11201, USA. 18 2Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks 19 Street, Toronto, ON, M5S 3B2, Canada. 20 3Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, 21 ON, M5S 2C6, Canada. 22 4Present address: Environmental Genomics Group, Max Planck Institute for 23 Evolutionary Biology, August-Thienemann-Str. -
Archaeological Tree-Ring Dating at the Millennium
P1: IAS Journal of Archaeological Research [jar] pp469-jare-369967 June 17, 2002 12:45 Style file version June 4th, 2002 Journal of Archaeological Research, Vol. 10, No. 3, September 2002 (C 2002) Archaeological Tree-Ring Dating at the Millennium Stephen E. Nash1 Tree-ring analysis provides chronological, environmental, and behavioral data to a wide variety of disciplines related to archaeology including architectural analysis, climatology, ecology, history, hydrology, resource economics, volcanology, and others. The pace of worldwide archaeological tree-ring research has accelerated in the last two decades, and significant contributions have recently been made in archaeological chronology and chronometry, paleoenvironmental reconstruction, and the study of human behavior in both the Old and New Worlds. This paper reviews a sample of recent contributions to tree-ring method, theory, and data, and makes some suggestions for future lines of research. KEY WORDS: dendrochronology; dendroclimatology; crossdating; tree-ring dating. INTRODUCTION Archaeology is a multidisciplinary social science that routinely adopts an- alytical techniques from disparate fields of inquiry to answer questions about human behavior and material culture in the prehistoric, historic, and recent past. Dendrochronology, literally “the study of tree time,” is a multidisciplinary sci- ence that provides chronological and environmental data to an astonishing vari- ety of archaeologically relevant fields of inquiry, including architectural analysis, biology, climatology, economics, -
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. -
ARTIFACTS and FEATURES DENDROCHRONOLOGY This
4/28/2004 ARTIFACTS AND FEATURES DENDROCHRONOLOGY This article is one of an occasional series discussing matters archaeological, especially with reference to the Maturango Museum. In previous articles we have talked about why chronologies are important in archaeology, and about a few qualitative techniques for establishing dates or sequences. Today we move on to another topic, quantitative chronological techniques. The first quantitative technique to be developed and applied in archaeology was dendrochronology, or tree-ring dating. It was developed in 1928 by A. E. Douglass of the University of Arizona, an astronomer who was studying sun-spot cycles. He theorized that climatic moisture was affected by the 11-year sun-spot cycle, and concluded that the evidence should be observable in tree rings. In the course of the studies he verified that the climatic sequence of wet and dry years does in fact leave a detectable pattern in the tree ring record: in general, wet years lead to wide rings and dry years to narrow rings. The important byproduct of this for archaeology is that the sequence of wet and dry years in a given locality never repeats itself, so the tree rings contain a unique signature which allows correlating between an old log and a new one, as long as there is some overlap. Douglass, to his credit, realized that his data would be useful to archaeologists, who at that time had no methods for assigning quantitative dates. Qualitative methods such as pottery seriation, stratigraphic excavation, and marker artifacts allow construction of sequences, but not absolute dating. Dendrochronology, for the first time, would allow an archaeologist to assign a date to the event of cutting down a tree to build a structure or use as fuel.