DOCSLIB.ORG

Species: Turning a Conundrum Into a Research Program

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Species: Turning a Conundrum Into a Research Program View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@University of Nebraska University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications from the Harold W. Manter Laboratory of Parasitology Parasitology, Harold W. Manter Laboratory of 6-1999 Species: Turning a Conundrum Into a Research Program Daniel R. Brooks University of Toronto, [email protected] Deborah A. McLennan University of Toronto E. C. Bernard University of Tennessee Follow this and additional works at: https://digitalcommons.unl.edu/parasitologyfacpubs Part of the Parasitology Commons Brooks, Daniel R.; McLennan, Deborah A.; and Bernard, E. C., "Species: Turning a Conundrum Into a Research Program" (1999). Faculty Publications from the Harold W. Manter Laboratory of Parasitology. 309. https://digitalcommons.unl.edu/parasitologyfacpubs/309 This Article is brought to you for free and open access by the Parasitology, Harold W. Manter Laboratory of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications from the Harold W. Manter Laboratory of Parasitology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Journal of Nematology 31(2):117–133. 1999. © The Society of Nematologists 1999. Species: Turning a Conundrum into a Research Program1 Daniel R. Brooks and Deborah A. McLennan2 Abstract: The most appropriate ontological basis for understanding the role of species in evolutionary biology is the Evolutionary Species Concept. The ESC is not an operational concept, but one version of the Phylogenetic Species Concept is. Linking the ontology of species with the epistemological basis of actual biological studies requires that we specify both a discovery mode for identifying collections of organisms that we believe are evolutionary species, and a series of evaluation criteria for assessing those entities we have discovered. Simply naming a collection of specimens, no matter how strong one’s evolutionary beliefs, is not sufficient for declaring that evolutionary species have been discovered. All operational historical species concepts represent discovery modes with minimal evaluation criteria; all operational non-dimensional species concepts represent evaluation criteria that do not specify discovery modes. Thus, both categories of knowledge are necessary and neither is sufficient for assigning species status. This leads naturally to a hierarchical research program in historical ecology, beginning with phylogenetic analysis of a group of entities postulated to be evolutionary species, which provides a productive arena for our arguments about species concepts. Key words: Evolutionary Species Concept, historical ecology, Phylogenetic Species Concept, phylog- eny, speciation. “Why is not all nature in confusion, in- isms grouped naturally into discrete species, stead of the species being, as we see them, species into genera, genera into families, well defined?” (Darwin, 1872:161). and so on until all living things were in- cluded in a single classification of life. Pre- AShort History of the Darwinian taxonomists, like all natural phi- “Species Problem” losophers of the day, argued that the only “real” entities were those that had immu- It is not uncommon for major scientific table spatio-temporal existence. Because of concepts to have ambiguous definitions. In their unchangeable nature, such bits of re- Biology, one such term is “species.” This ality could be grouped into “classes” de- dilemma pre-dates Darwin (Stevens, 1992). fined by the fixed properties of their com- Initially, the “species” was simply a category ponents. Classic examples of such “real” in classifications, the least inclusive group of entities, which at the time were called “spe- organisms to be recognized formally. That cies,” are “hydrogen” and “gold.” Like the biosphere was organized into an in- these other natural kinds, biological species ternested hierarchy of species and groups of existed and conformed to a single hierarchi- species was thought to be self-evident. It was cal classification simply because it pleased simply the nature of the world that organ- the Creator for it to be so. In the absence of any causal principles explaining the taxo- Received for publication 20 November 1998. nomic hierarchy linking species together, 1 Symposium paper presented at the 37th Annual Meeting of the Society of Nematologists, 20–24 July 1998, St. Louis, MO. pre-Darwinian taxonomists relied on aes- 2 Centre for Comparative Biology and Biodiversity, Depart- thetics, intuition, and personal judgement ment of Zoology, University of Toronto, Toronto, Ontario M5S 3G5, Canada. to make decisions. E-mail: [email protected], mclennan@zoo. Darwin (1859) complicated things by sug- utoronto.ca Development of the perspective presented herein has been gesting that while organisms could indeed helped substantially by an enormous amount of published lit- be grouped naturally into species, these bio- erature appearing during the past 25 years, in addition to dis- cussions with Kare Bremer, John Collier, Joel Cracraft, Michael logical “species” were not immutable. Dar- Donoghue, Cyril Finnegan, Darryl Frost, William Fink, Vicki win’s belief in both the reality and the evo- Funk, Robert Geesink, David Hull, Arnold Kluge, Diedel Kor- net, Brian Maurer, Richard Mayden, Jack Maze, Brent Mishler, lutionary nature of biological species was Stan Salthe, Geoffrey Scudder, Jonathan Smith, Hans-Erik based on several empirical observations. Wanntorp, Quentin Wheeler, E. O. Wiley, and Rino Zandee. The authors especially thank Virginia Ferris for the invitation to First, comparing fossil and living species sug- participate in the symposium on species concepts. This study gested that the species populating the was supported by operating grants from the Natural Sciences and Engineering Research Council (NSERC) of Canada. planet today are not the same as those popu- This paper was edited by E. C. Bernard. lating the planet in the past. Second, the 117 118 Journal of Nematology, Volume 31, No. 2, June 1999 world today is not populated by a small num- Darwin’s comments: “Hence, in determin- ber of species widely distributed in many dif- ing whether a form should be ranked as a ferent habitats in many different parts of the species or a variety, the opinion of natural- world; different species live in different parts ists having sound judgement and wide expe- of the world. And third, all living and extinct rience seems the only guide to follow. We species fit into a single hierarchical classifi- must, however, in many cases, decide by a cation that looks like a genealogy. Using majority of naturalists, for well-marked and perhaps the original form of the “Wiley Cri- well-known varieties can be named which terion” (Brooks and McLennan, 1991), Dar- have not been ranked as species by at least win suggested that if it looked like a geneal- some competent judges” (Darwin, 1872). ogy, it was one. Such concerns still preoccupy the minds This conclusion led Darwin to his first of some taxonomists (Grant, 1985). In the theory—that all species on this planet were second half of the 20th century, evolutionary related to each other through a single com- taxonomy (Mayr, 1969) epitomized the pre- mon history of descent with modification: Darwinian view that taxonomy was partly sci- phylogeny. It is not mere happenstance that ence and partly art form, with a sizeable the only illustration Darwin ever placed in component of personal judgement and in- any edition of Origin of Species was a phylo- tuition involved in trying to justify taxo- genetic tree (Bowler, 1996). Darwin had cre- nomic decisions in terms of evolutionary ated a dual role for species in biology. In principles. Phenetics, or numerical tax- addition to being units of classification, spe- onomy (Sneath and Sokal, 1973; Levins, cies were now also units of evolutionary pro- 1979), by contrast, abandoned all efforts to cess; identifying and classifying species was provide a link between taxonomy and evo- not simply a matter of convenience, it was lution by advocating purely empirical classi- explanatory. From the statements about spe- fication procedures having no particular cies in Origin of Species, it is clear that Darwin connection with evolutionary principles. recognized this duality. Biologists have at- Hull (1965) presciently described taxonomy tempted to resolve this dualism in a variety at this time as the inheritor of 2,000 years of of ways during the past 140 years, but it still stasis resulting from the notion that all units exists. For example, Ereshevsky (1992) of classification had to have uniquely defin- stated “Biological systematists attempt to ing (and hence unchanging) characters, an provide a taxonomy of the world’s organic indication that the Darwinian revolution still diversity. Evolutionary biologists attempt to had not penetrated deeply into taxonomic explain why that diversity exists.” practice. Following the publication of Origin of Spe- Other biologists have dealt with Darwin’s cies, taxonomists, by and large, continued to dualism by attempting to replace the pre- concentrate on species as units of classifi- Darwinian taxonomic concept of species cation and tended to ignore evolutionary with one based strictly in evolutionary principles, invoking these principles only to mechanisms or by trying to eliminate the justify taxonomic decisions made follow- species concept altogether. Darwin wrote ing traditional
Load more

Recommended publications
  • A Stochastic Model of Language Evolution That Incorporates Homoplasy and Borrowing
    A STOCHASTIC MODEL OF LANGUAGE EVOLUTION THAT INCORPORATES HOMOPLASY AND BORROWING TANDY WARNOW, STEVEN N. EVANS, DONALD RINGE, AND LUAY NAKHLEH 1. Introduction The inference of evolutionary history, whether in biology or in lin- guistics, is aided by a carefully considered model of the evolutionary process and a reconstruction method which is expected to produce a reasonably accurate estimation of the true evolutionary history when the real data match the model assumptions and are of sufficient quan- tity. In molecular systematics (i.e., the inference of evolutionary his- tories from molecular data), much of the research effort has focused in two areas: first, the development of increasingly parameter rich models of molecular sequence evolution, and second, the development of increasingly sophisticated software tools and algorithms for recon- structing phylogenies under these models. The plethora of software for reconstructing phylogenies from molecular data is staggering. By com- parison, much less has been done in historical linguistics in terms of developing statistical models of character evolution or reconstruction methods, suggesting that there is perhaps much to be gained by doing so. To date, although some models have been proposed for language evo- lution, all have failed in some significant ways. In particular, linguistic models either explicitly or implicitly have assumed that no homoplasy (i.e., parallel evolution and/or back–mutation) occurs (see for exam- ple (Ringe et al. , 2002; Taylor et al. , 2000; Warnow, 1997)). Most, but not all, have not modelled borrowing between languages. In this paper, we go beyond earlier models by explicitly incorporating both homoplasy and borrowing into our model.
    [Show full text]
  • Preliminary Phylogeny of Diplostephium (Asteraceae): Speciation Rate and Character Evolution
    NUMBER 15 VARGAS AND MADRIN˜ A´ N: SPECIATION AND CHARACTER EVOLUTION OF DIPLOSTEPHIUM 1 PRELIMINARY PHYLOGENY OF DIPLOSTEPHIUM (ASTERACEAE): SPECIATION RATE AND CHARACTER EVOLUTION Oscar M. Vargas1,2 and Santiago Madrin˜a´n2 1Section of Integrative Biology and the Plant Resources Center, The University of Texas, 205 W 24th St., Stop CO930, Austin, Texas 78712 U.S.A., email: [email protected] 2Laboratorio de Bota´nica y Sistema´tica Universidad de los Andes, Apartado Ae´reo 4976, Bogota´, D. C., Colombia Abstract: Diplostephium comprises 111 neotropical species that live in high elevation habitats from Costa Rica to Chile. Primarily Andean, the genus seems to have undergone an adaptive radiation indicated by its high number of species, broad morphological variation, and diversification primarily in an ecosystem (pa´ramo) that formed within the last 2–5 my. Internal transcriber spacer (ITS) sequences and several chloroplast markers, rpoB, rpoC1, and psbA-trnH were sequenced in order to infer a preliminary phylogeny of the genus. The chloroplast regions showed no significant variation within the genus. New ITS data were therefore analyzed together with published sequences for generating a topology. Results suggest that Diplostephium and other South American genera comprise a polytomy within which a previously described North American clade is nested. Monophyly of Diplostephium was neither supported nor rejected, but the formation of a main crown clade using different methods of analysis suggests that at least a good portion of the genus is monophyletic. A Shimodaira-Hasegawa test comparing the topology obtained and a constrained one forcing Diplostephium to be monophyletic showed no significant difference between them.
    [Show full text]
  • 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.
    [Show full text]
  • Trait-Based Extinction Catches the Red Queen Napping During the Cambrian P
    COMMENTARY Trait-based extinction catches the Red Queen napping during the Cambrian P. David Polly1 changes, estimating the rates of speciation Department of Geological Sciences, Indiana University, Bloomington, IN 47405 and extinction inside and outside that node, and repeating the exercise for all traits (8). The tenuous balance between speciation and or otherwise adapting faster than the Red The number of candidate trait changes in extinction governs the rise and fall of di- Queen’s pace of constant extinction expected even one clade is large, 275 in the early tet- versity within clades, from which have in resource-limited environments (5, 6). In rapod dataset alone (9). Furthermore, flaws emerged the sweeping changes in Earth’s PNAS, Wagner and Estabrook (7) ask in the phylogeny can lead to misinterpreta- standing biodiversity since life’sorigin(1, whether diversification was associated with tions about the link between diversification 2). In a clade where speciation and extinction the evolution of new traits and, if so, did and traits, and phylogenetic analyzes of ex- are equally likely, net diversity remains con- the probability of speciation go up in clades tinct metazoan taxa are sparse compared with their immense Phanerozoic diversity. stant; when the rate of speciation exceeds that have the new trait, did the group’srateof To meet these challenges, the authors extinction, diversity increases exponentially; trait evolution go up, did extinction go up in approached the problem indirectly by look- and when the chance of extinction outweighs the clades that do not have the trait, or some ing at the sequence of trait combinations in speciation, then diversity falls, resulting ulti- combination of these.
    [Show full text]
  • Convergent Evolution of Behavior in an Adaptive Radiation of Hawaiian Web-Building Spiders
    Convergent evolution of behavior in an adaptive radiation of Hawaiian web-building spiders Todd A. Blackledge† and Rosemary G. Gillespie Department of Environmental Science, Policy, and Management, Division of Insect Biology, 201 Wellman Hall, University of California, Berkeley, CA 94720 Communicated by Thomas W. Schoener, University of California, Davis, CA, October 6, 2004 (received for review March 22, 2004) Species in ecologically similar habitats often display patterns of such that differences in web shape can indicate differences in divergence that are strikingly comparable, suggesting that natural how spiders are using resources (17, 19–21). We assess the selection can lead to predictable evolutionary change in commu- relative predictability of behavioral evolution within the adap- nities. However, the relative importance of selection as an agent tive radiation of Hawaiian orb-weaving Tetragnatha by compar- mediating in situ diversification, versus dispersal between habi- ing the web architectures of species, both within islands and tats, cannot be addressed without knowledge of phylogenetic among communities on different islands, and by examining the history. We used an adaptive radiation of spiders within the historical diversification of those behaviors. Hawaiian Islands to test the prediction that species of spiders on different islands would independently evolve webs with similar Materials and Methods architectures. Tetragnatha spiders are the only nocturnal orb- Focal Localities. We studied spiders in focal localities on three weaving spiders endemic to the Hawaiian archipelago, and mul- different islands, each of which consisted of mature mesic to wet tiple species of orb-weaving Tetragnatha co-occur within mesic forest vegetation but varied in age according to island (22): and wet forest habitats on each of the main islands.
    [Show full text]
  • Inferring and Testing Hypotheses of Cladistic Character Dependence by Using Character Compatibility F
    Marshall University Marshall Digital Scholar Biological Sciences Faculty Research Biological Sciences 9-2001 Inferring and Testing Hypotheses of Cladistic Character Dependence by Using Character Compatibility F. Robin O’Keefe Marshall University, [email protected] Peter J. Wagner Follow this and additional works at: http://mds.marshall.edu/bio_sciences_faculty Part of the Animal Sciences Commons, Biochemistry, Biophysics, and Structural Biology Commons, and the Biology Commons Recommended Citation O’Keefe, F. R., and P. J. Wagner. 2001. Inferring and testing hypotheses of cladistic character dependence by using character compatibility. Syst. Biol. 50:657–675. This Article is brought to you for free and open access by the Biological Sciences at Marshall Digital Scholar. It has been accepted for inclusion in Biological Sciences Faculty Research by an authorized administrator of Marshall Digital Scholar. For more information, please contact [email protected], [email protected]. Syst. Biol. 50(5):657–675, 2001 Inferring and Testing Hypotheses of Cladistic Character Dependence by Using Character Compatibility F. ROBIN O’KEEFE1 AND PETER J. WAGNER2 1 Department of Anatomy, New York College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, New York 11568-8000 , USA; E-mail: [email protected] 2Department of Geology, Field Museum of Natural History, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605, USA; E-mail: [email protected] Abstract.—The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complemen- tary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference.
    [Show full text]
  • Phylogeny and Character Evolution in the Dacrymycetes, and Systematics of Unilacrymaceae and Dacryonaemataceae Fam
    Persoonia 44, 2020: 161–205 ISSN (Online) 1878-9080 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE https://doi.org/10.3767/persoonia.2020.44.07 Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov. J.C. Zamora1,2, S. Ekman1 Key words Abstract We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1, RPB2, TEF-1α, 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted Carotenoids genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymy­ coalescence analyses cetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, cytology to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, Dacrymycetes and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate Dacryonaema for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacu- species delimitations olar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial Unilacryma emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/ marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named.
    [Show full text]
  • Trait-Based Extinction Catches the Red Queen Napping During the Cambrian P
    COMMENTARY COMMENTARY Trait-based extinction catches the Red Queen napping during the Cambrian P. David Polly1 changes, estimating the rates of speciation Department of Geological Sciences, Indiana University, Bloomington, IN 47405 and extinction inside and outside that node, and repeating the exercise for all traits (8). The tenuous balance between speciation and or otherwise adapting faster than the Red The number of candidate trait changes in extinction governs the rise and fall of di- Queen’s pace of constant extinction expected even one clade is large, 275 in the early tet- versity within clades, from which have in resource-limited environments (5, 6). In rapod dataset alone (9). Furthermore, flaws emerged the sweeping changes in Earth’s PNAS, Wagner and Estabrook (7) ask in the phylogeny can lead to misinterpreta- standing biodiversity since life’sorigin(1, whether diversification was associated with tions about the link between diversification 2). In a clade where speciation and extinction the evolution of new traits and, if so, did and traits, and phylogenetic analyzes of ex- are equally likely, net diversity remains con- the probability of speciation go up in clades tinct metazoan taxa are sparse compared with their immense Phanerozoic diversity. stant; when the rate of speciation exceeds that have the new trait, did the group’srateof To meet these challenges, the authors extinction, diversity increases exponentially; trait evolution go up, did extinction go up in approached the problem indirectly by look- and when the chance of extinction outweighs the clades that do not have the trait, or some ing at the sequence of trait combinations in speciation, then diversity falls, resulting ulti- combination of these.
    [Show full text]
  • Phylogenetic Trees and Their Analysis
    City University of New York (CUNY) CUNY Academic Works All Dissertations, Theses, and Capstone Projects Dissertations, Theses, and Capstone Projects 2-2014 Phylogenetic Trees and Their Analysis Eric Ford Graduate Center, City University of New York How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/gc_etds/37 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] Phylogenetic Trees and Their Analysis by ERIC FORD A dissertation submitted to the Graduate Faculty in Computer Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy, The City University of New York 2014 Copyright c by Eric Ford 2013 ii This manuscript has been read and accepted for the Graduate Faculty in Computer Science in satisfaction of the dissertation requirement for the degree of Doctor of Philosophy Katherine St. John Date Chair of Examining Committee Robert Haralick Date Executive Officer, Dept. of Computer Science Ward Wheeler Amotz Bar-Noy Daniel Gusfield Supervisory Committee THE CITY UNIVERSITY OF NEW YORK iii ABSTRACT Phylogenetic Trees and Their Analysis by Eric Ford Advisor: Katherine St. John Determining the best possible evolutionary history, the lowest-cost phylogenetic tree, to fit a given set of taxa and character sequences using maximum parsimony is an active area of research due to its underlying importance in understanding biological processes. As several steps in this process are NP-Hard when using popular, biologically-motivated optimality criteria, significant amounts of resources are dedicated to both both heuristics and to making exact methods more computationally tractable.
    [Show full text]
  • Tracking Character Evolution and Biogeographic History Through Time in Cornaceae—Does Choice of Methods Matter? Qiu-Yun (Jenny) XIANG* David T
    Journal of Systematics and Evolution 46 (3): 349–374 (2008) doi: 10.3724/SP.J.1002.2008.08056 (formerly Acta Phytotaxonomica Sinica) http://www.plantsystematics.com Tracking character evolution and biogeographic history through time in Cornaceae—Does choice of methods matter? Qiu-Yun (Jenny) XIANG* David T. THOMAS (Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USA) Abstract This study compares results on reconstructing the ancestral state of characters and ancestral areas of distribution in Cornaceae to gain insights into the impact of using different analytical methods. Ancestral charac- ter state reconstructions were compared among three methods (parsimony, maximum likelihood, and stochastic character mapping) using MESQUITE and a full Bayesian method in BAYESTRAITS and inferences of ancestral area distribution were compared between the parsimony-based dispersal-vicariance analysis (DIVA) and a newly developed maximum likelihood (ML) method. Results indicated that among the six inflorescence and fruit char- acters examined, “perfect” binary characters (no homoplasy, no polymorphism within terminals, and no missing data) are little affected by choice of method, while homoplasious characters and missing data are sensitive to methods used. Ancestral areas at deep nodes of the phylogeny are substantially different between DIVA and ML and strikingly different between analyses including and excluding fossils at three deepest nodes. These results, while raising caution in making conclusions on trait evolution and historical biogeography using conventional methods, demonstrate a limitation in our current understanding of character evolution and biogeography. The biogeographic history favored by the ML analyses including fossils suggested the origin and early radiation of Cornus likely occurred in the late Cretaceous and earliest Tertiary in Europe and intercontinental disjunctions in three lineages involved movements across the North Atlantic Land Bridge (BLB) in the early and mid Tertiary.
    [Show full text]
  • Macroevolutionary Analysis of Discrete Character Evolution Using Parsimony-Informed Likelihood
    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.07.897603; this version posted January 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Macroevolutionary analysis of discrete character evolution using parsimony-informed likelihood 2 3 Michael C. Grundler1,* and Daniel L. Rabosky1 4 5 1 Museum of Zoology and Department of Ecology and Evolutionary Biology, University of 6 Michigan, Ann Arbor, MI 48109-1079, USA 7 8 * Corresponding author: [email protected] 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.07.897603; this version posted January 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 24 ABSTRACT 25 Rates of character evolution in macroevolutionary datasets are typically estimated by 26 maximizing the likelihood function of a continuous-time Markov chain (CTMC) model of 27 character evolution over all possible histories of character state change, a technique known as 28 maximum average likelihood. An alternative approach is to estimate ancestral character states 29 independently of rates using parsimony and to then condition likelihood-based estimates of 30 transition rates on the resulting ancestor-descendant reconstructions.
    [Show full text]
  • Convergent Evolution of Life Habit and Shell Shape in Scallops (Bivalvia: Pectinidae) with a Description of a New Genus Alvin Alejandrino Iowa State University
    Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Convergent evolution of life habit and shell shape in scallops (Bivalvia: Pectinidae) with a description of a new genus Alvin Alejandrino Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Biology Commons, and the Evolution Commons Recommended Citation Alejandrino, Alvin, "Convergent evolution of life habit and shell shape in scallops (Bivalvia: Pectinidae) with a description of a new genus" (2014). Graduate Theses and Dissertations. 14056. https://lib.dr.iastate.edu/etd/14056 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Convergent evolution of life habit and shell shape in scallops (Bivalvia: Pectinidae) with a description of a new genus by Alvin Alejandrino A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Ecology and Evolutionary Biology i Program of Study Committee: Jeanne M. Serb, Major Professor Dean C. Adams Dennis Lavrov Nicole Valenzuela Kevin J. Roe Iowa State University Ames, Iowa 2014 Copyright © Alvin Alejandrino, 2014. All rights reserved. ii DEDICATION To my brother, Edward Andrew Haffner (May 19, 1986 – December 26, 2011). You showed me that family and happiness are the most important things in life. I miss and love you.
    [Show full text]