Convergent Evolution of Behavior in an Adaptive Radiation of Hawaiian Web-Building Spiders
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Phylogenetic Analysis of Anostracans (Branchiopoda: Anostraca) Inferred from Nuclear 18S Ribosomal DNA (18S Rdna) Sequences
MOLECULAR PHYLOGENETICS AND EVOLUTION Molecular Phylogenetics and Evolution 25 (2002) 535–544 www.academicpress.com Phylogenetic analysis of anostracans (Branchiopoda: Anostraca) inferred from nuclear 18S ribosomal DNA (18S rDNA) sequences Peter H.H. Weekers,a,* Gopal Murugan,a,1 Jacques R. Vanfleteren,a Denton Belk,b and Henri J. Dumonta a Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium b Biology Department, Our Lady of the Lake University of San Antonio, San Antonio, TX 78207, USA Received 20 February 2001; received in revised form 18 June 2002 Abstract The nuclear small subunit ribosomal DNA (18S rDNA) of 27 anostracans (Branchiopoda: Anostraca) belonging to 14 genera and eight out of nine traditionally recognized families has been sequenced and used for phylogenetic analysis. The 18S rDNA phylogeny shows that the anostracans are monophyletic. The taxa under examination form two clades of subordinal level and eight clades of family level. Two families the Polyartemiidae and Linderiellidae are suppressed and merged with the Chirocephalidae, of which together they form a subfamily. In contrast, the Parartemiinae are removed from the Branchipodidae, raised to family level (Parartemiidae) and cluster as a sister group to the Artemiidae in a clade defined here as the Artemiina (new suborder). A number of morphological traits support this new suborder. The Branchipodidae are separated into two families, the Branchipodidae and Ta- nymastigidae (new family). The relationship between Dendrocephalus and Thamnocephalus requires further study and needs the addition of Branchinella sequences to decide whether the Thamnocephalidae are monophyletic. Surprisingly, Polyartemiella hazeni and Polyartemia forcipata (‘‘Family’’ Polyartemiidae), with 17 and 19 thoracic segments and pairs of trunk limb as opposed to all other anostracans with only 11 pairs, do not cluster but are separated by Linderiella santarosae (‘‘Family’’ Linderiellidae), which has 11 pairs of trunk limbs. -
Investgating Determinants of Phylogeneic Accuracy
IMPACT OF MOLECULAR EVOLUTIONARY FOOTPRINTS ON PHYLOGENETIC ACCURACY – A SIMULATION STUDY Dissertation Submitted to The College of Arts and Sciences of the UNIVERSITY OF DAYTON In Partial Fulfillment of the Requirements for The Degree Doctor of Philosophy in Biology by Bhakti Dwivedi UNIVERSITY OF DAYTON August, 2009 i APPROVED BY: _________________________ Gadagkar, R. Sudhindra Ph.D. Major Advisor _________________________ Robinson, Jayne Ph.D. Committee Member Chair Department of Biology _________________________ Nielsen, R. Mark Ph.D. Committee Member _________________________ Rowe, J. John Ph.D. Committee Member _________________________ Goldman, Dan Ph.D. Committee Member ii ABSTRACT IMPACT OF MOLECULAR EVOLUTIONARY FOOTPRINTS ON PHYLOGENETIC ACCURACY – A SIMULATION STUDY Dwivedi Bhakti University of Dayton Advisor: Dr. Sudhindra R. Gadagkar An accurately inferred phylogeny is important to the study of molecular evolution. Factors impacting the accuracy of a phylogenetic tree can be traced to several consecutive steps leading to the inference of the phylogeny. In this simulation-based study our focus is on the impact of the certain evolutionary features of the nucleotide sequences themselves in the alignment rather than any source of error during the process of sequence alignment or due to the choice of the method of phylogenetic inference. Nucleotide sequences can be characterized by summary statistics such as sequence length and base composition. When two or more such sequences need to be compared to each other (as in an alignment prior to phylogenetic analysis) additional evolutionary features come into play, such as the overall rate of nucleotide substitution, the ratio of two specific instantaneous, rates of substitution (rate at which transitions and transversions occur), and the shape parameter, of the gamma distribution (that quantifies the extent of iii heterogeneity in substitution rate among sites in an alignment). -
Eidesstattliche Erklärung
ZENTRUM FÜR BIODIVERSITÄT UND NACHHALTIGE LANDNUTZUNG SEKTION BIODIVERSITÄT, ÖKOLOGIE UND NATURSCHUTZ CENTRE OF BIODIVERSITY AND SUSTAINABLE LAND USE SECTION: BIODIVERSITY, ECOLOGY AND NATURE CONSERVATION Mitochondrial genomes and the complex evolutionary history of the cercopithecine tribe Papionini Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultäten der Georg-August-Universität zu Göttingen vorgelegt von Dipl. Biol. Rasmus Liedigk aus Westerstede Göttingen, September 2014 Referent: PD Dr. Christian Roos Korreferent: Prof. Dr. Eckhard Heymann Tag der mündlichen Prüfung: 19.9.2014 Table of content 1 General introduction .............................................................................................. 1 1.1 An introduction to phylogenetics ....................................................................... 1 1.2 Tribe Papionini – subfamily Cercopithecinae ..................................................... 3 1.2.1 Subtribe Papionina.................................................................................... 4 1.2.2 Subtribe Macacina, genus Macaca ........................................................... 5 1.3 Papionin fossils in Europe and Asia................................................................... 7 1.3.1 Fossils of Macaca ..................................................................................... 8 1.3.2 Fossils of Theropithecus ........................................................................... 9 1.4 The mitochondrial genome and its -
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. -
Genetics 540 Winter, 2001 Models of DNA Evolution – Part 2 Joe Felsenstein Department of Genetics University of Washington
Genetics 540 Winter, 2001 Models of DNA evolution { part 2 Joe Felsenstein Department of Genetics University of Washington joe@genetics A model of variation in evolutionary rates among sites The basic idea is that the rate at each site is drawn independently from a distribution of rates. The most widely used choice is the Gamma distribution, which has density function (if its mean is 1): αα rα 1 e α r f(r) = − − Γ(α) Unrealistic aspects of the model: • There is no reason, aside from mathematical convenience, to assume that the Gamma is the right distribution. A common variation is to assume there is a separate probability f0 of having rate 0. • Rates at different sites appear to be correlated, which this model does not allow. • Rates are not constant throughout evolution { they change with time. α = 0.25 cv = 2 α = 11.1111 α = 1 cv = 0.3 frequency cv = 1 0 0.5 1 1.5 2 rate Gamma distributions with mean 1 and different coefficients of variation (standard deviation / mean). α = 1=CV 2 is the \shape parameter" of the Gamma distribution Hidden Markov Models These are the most widely used models allowing rate variation to be correlated along the sequence. We assume: • There are a finite number of rates, m. Rate i is ri. • There are probabilities pi of a site having rate i. • A process not visible to us (\hidden") assigns rates to sites. It is a Markov process working along the sequence. For example it might have transition probability Prob (jji) of changing to rate j in the next site, given that it is at rate i in this site. -
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. -
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. -
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. -
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. -
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. -
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. -
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.