Molecular Phylogenetic Analysis of Evolutionary Trends in Stonefly Wing Structure and Locomotor Behavior

Total Page:16

File Type:pdf, Size:1020Kb

Molecular Phylogenetic Analysis of Evolutionary Trends in Stonefly Wing Structure and Locomotor Behavior Molecular phylogenetic analysis of evolutionary trends in stonefly wing structure and locomotor behavior Michael A. Thomas, Kathleen A. Walsh, Melisande R. Wolf, Bruce A. McPheron, and James H. Marden* 208 Mueller Laboratory, Department of Biology, Pennsylvania State University, University Park, PA 16802 Edited by May R. Berenbaum, University of Illinois at Urbana–Champaign, Urbana, IL, and approved September 15, 2000 (received for review June 27, 2000) Insects in the order Plecoptera (stoneflies) use a form of two- evolutionary reduction in wing structural complexity. Surface dimensional aerodynamic locomotion called surface skimming to skimming and reduced wing complexity may have evolved as move across water surfaces. Because their weight is supported by correlated traits during an evolutionary reduction in flight water, skimmers can achieve effective aerodynamic locomotion proficiency in certain lineages of modern stoneflies. even with small wings and weak flight muscles. These mechanical To determine the evolutionary history of stonefly skimming features stimulated the hypothesis that surface skimming may and wing structural complexity, it is necessary to examine how have been an intermediate stage in the evolution of insect flight, these traits are distributed across the plecopteran phylogeny. which has perhaps been retained in certain modern stoneflies. This type of analysis has already been attempted for surface Here we present a phylogeny of Plecoptera based on nucleotide skimming (15), which resulted in the conclusion that skimming sequence data from the small subunit rRNA (18S) gene. By mapping behavior is most likely a derived, apomorphic condition, i.e., a locomotor behavior and wing structural data onto the phylogeny, relatively recent loss of flight. However, that analysis had two we distinguish between the competing hypotheses that skimming serious shortcomings. First, the morphological characters used is a retained ancestral trait or, alternatively, a relatively recent loss to construct that phylogeny were not compared with homologous of flight. Our results show that basal stoneflies are surface skim- traits of outgroup taxa to determine their polarity (ancestral vs. mers, and that various forms of surface skimming are distributed derived; ref. 16). Polarities were assigned based on resemblance widely across the plecopteran phylogeny. Stonefly wings show to assumed ancestral conditions. This is problematic, and the evolutionary trends in the number of cross veins and the thickness resulting tree has limited utility for assessing evolutionary his- of the cuticle of the longitudinal veins that are consistent with tory. Second, the analysis assumed that skimming was restricted elaboration and diversification of flight-related traits. These data to the single species in which the behavior had been originally support the hypothesis that the first stoneflies were surface described (3), despite the fact that presence or absence of skimmers, and that wing structures important for aerial flight have skimming in other stonefly taxa had not been determined. become elaborated and more diverse during the radiation of Lacking even a rudimentary knowledge of the taxonomic dis- modern stoneflies. tribution of the trait in question, the analysis and conclusions are questionable. nsect flight is an example of a complex trait whose origin is Here we reexamine this question by using a rooted phyloge- Idifficult to explain by using a model that depends on gradual netic analysis based on DNA sequence data from stoneflies and progression through intermediate stages (1, 2). How can tiny a number of outgroup taxa. Mapping wing structural data and wings, simple wing hinges, and weak muscles provide a func- skimming behavior onto this phylogeny allows us to test hypoth- tional advantage over no wings at all? A novel solution to this eses about the evolutionary direction of locomotor behavior and riddle was recently provided by the discovery of surface skim- wing structural complexity. ming, a nonflying form of aerodynamic locomotion used by Methods certain stoneflies (Plecoptera) and mayflies (Ephemeroptera) to move in two dimensions across water surfaces (3–7). By flapping Phylogenetic Analysis. The small subunit rRNA (18S) gene was their wings or by using them as nonflapping sails while their sequenced for 34 stonefly species representing all families of weight is supported by water, skimmers can achieve effective Plecoptera (GenBank accession nos. AF311439–AF311472; a aerodynamic locomotion even with small wings and weak flight complete list of taxa and collection information can be found in muscles (3, 4). Table 1, which is published as supplemental data on the PNAS Surface skimming is now widely accepted as a plausible web site, www.pnas.org). An additional stonefly sequence (Me- mechanical model for flight evolution (8–11), but there is soperlina pecirai; Perlodidae) was obtained from GenBank (ac- cession no. U68400). DNA was extracted by using standard considerably less support for the suggestion (3, 4) that skimming ͞ in modern stoneflies is a retained ancestral trait. Many pterygote phenol chloroform protocols for alcohol-preserved material (17). Amplification of the 18S gene by the PCR used two insects have lost the ability to fly, including numerous stonefly Ј species that are wingless or possess greatly reduced wings. There oligonucleotide primers, rev18G (5 -AGGGCAAGTCTGGT- also appears to have been an evolutionary reduction in the number of cross veins in the wings of stoneflies in the super- This paper was submitted directly (Track II) to the PNAS office. family Nemouroidea (12), the clade in which skimming was first Abbreviations: NJ, neighbor joining; ME, minimum evolution; ML, maximum likelihood; described. Cross veins are structural elements that link the main MP, maximum parsimony. longitudinal veins; in some locations they stiffen the wing, Data deposition: The sequences reported in this paper have been deposited in the GenBank whereas in others they contribute to active and passive defor- database (accession nos. AF311439–AF311472). mations of the wing planiform that enhance aerodynamic per- *To whom reprint requests should be addressed. E-mail: [email protected]. formance (13, 14). The stonefly taxa that are traditionally The publication costs of this article were defrayed in part by page charge payment. This thought to be the basal group have wings with abundant cross article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. veins, as do other basal pterygotes (mayflies, dragonflies, and §1734 solely to indicate this fact. various extinct fossil lineages), thereby suggesting that particular Article published online before print: Proc. Natl. Acad. Sci. USA, 10.1073͞pnas.230296997. lineages of more recently evolved stoneflies have undergone an Article and publication date are at www.pnas.org͞cgi͞doi͞10.1073͞pnas.230296997 13178–13183 ͉ PNAS ͉ November 21, 2000 ͉ vol. 97 ͉ no. 24 Downloaded by guest on October 2, 2021 GCCA) and 18L (5Ј-CACCTACGGAAACCTTGTTAC- GACTT), generating an approximately 1,300-nt fragment. Sequencing primers included the two PCR primers and two internal primers 18H (5Ј-TCAATTCCTTTAAGTTTGAGC) and rev18H (5Ј-GCTGAAACTTAAAGGAATTGA), which generated sequence fragments of approximately 700 nucleotides in length. Cycle-sequencing reactions were performed by using 3Ј BigDye-labeled dideoxynucleotide triphosphates and run on an Applied Biosystems Prism 377 DNA Sequencer. Raw data were analyzed by using the DNA STAR SEQMAN II sequence analysis program (DNAstar, Madison, WI). Outgroup taxa used to root the phylogeny were selected by using a relative apparent synapomorphy analysis (RASA; ref. 18), which identifies outgroups that maximize the ratio of informative phylogenetic signal to uninformative noise, thereby increasing the probability that the correct phylogeny is recov- ered. Of the outgroup combinations we tested (a list can be found in Supplemental Table 2 published on the PNAS web site, www.pnas.org), a diverse set of Hemiptera, Orthoptera, Der- maptera, Phasmatodea, Embioptera, Grylloblattodea, and Blat- todea (GenBank accession nos. U06478, U06480, U09207, U06477, Z97573, Z97574, Z97594, Z97561, Z97575, Z97593, ϭ Z97569, and Z97592) yielded the highest tRASA statistic (tRASA Ͻ Fig. 1. (A) Regions of stonefly wings from which cross veins were counted 31.814; P 0.001). and location of the chordwise cross section used for measurements of vein Sequences were aligned by using the CLUSTAL W alignment morphology. (B and C) Examples of cross sections of longitudinal wing veins model (19). The alignment consisted of 1,696 sites, including and the measurements taken for cuticle thickness. B shows the medial vein of gaps. A total of 578 sites, primarily in one large hypervariable a relatively basal species, Taeniopteryx burksi; C shows the medial vein of the region, were unalignable and therefore were excluded from our relatively derived species, Pteronarcella badia. analyses (sites 122–510, 591–600, 662–670, 774–776, 1182–1240, 1353–1362, 1564–1608, and 1644–1696). The analyzed data set consisted of 331 variable (133 nonparsimony informative and 198 subcostal or radial vein (hereafter referred to as costal cross parsimony informative) and 787 constant sites. Average nucle- veins) and those between the anterior cubital vein and both the otide frequencies estimated by PAUP were 24:23:28:25 medial vein and the posterior cubital vein (hereafter referred to (A:C:G:T). There was no significant
Recommended publications
  • 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).
    [Show full text]
  • Phylogeny Inference Based on Parsimony and Other Methods Using Paup*
    8 Phylogeny inference based on parsimony and other methods using Paup* THEORY David L. Swofford and Jack Sullivan 8.1 Introduction Methods for inferring evolutionary trees can be divided into two broad categories: thosethatoperateonamatrixofdiscretecharactersthatassignsoneormore attributes or character states to each taxon (i.e. sequence or gene-family member); and those that operate on a matrix of pairwise distances between taxa, with each distance representing an estimate of the amount of divergence between two taxa since they last shared a common ancestor (see Chapter 1). The most commonly employed discrete-character methods used in molecular phylogenetics are parsi- mony and maximum likelihood methods. For molecular data, the character-state matrix is typically an aligned set of DNA or protein sequences, in which the states are the nucleotides A, C, G, and T (i.e. DNA sequences) or symbols representing the 20 common amino acids (i.e. protein sequences); however, other forms of discrete data such as restriction-site presence/absence and gene-order information also may be used. Parsimony, maximum likelihood, and some distance methods are examples of a broader class of phylogenetic methods that rely on the use of optimality criteria. Methods in this class all operate by explicitly defining an objective function that returns a score for any input tree topology. This tree score thus allows any two or more trees to be ranked according to the chosen optimality criterion. Ordinarily, phylogenetic inference under criterion-based methods couples the selection of The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme (eds.).
    [Show full text]
  • 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.
    [Show full text]
  • Clustering and Phylogenetic Approaches to Classification: Illustration on Stellar Tracks Didier Fraix-Burnet, Marc Thuillard
    Clustering and Phylogenetic Approaches to Classification: Illustration on Stellar Tracks Didier Fraix-Burnet, Marc Thuillard To cite this version: Didier Fraix-Burnet, Marc Thuillard. Clustering and Phylogenetic Approaches to Classification: Il- lustration on Stellar Tracks. 2014. hal-01703341 HAL Id: hal-01703341 https://hal.archives-ouvertes.fr/hal-01703341 Preprint submitted on 7 Feb 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Clustering and Phylogenetic Approaches to Classification: Illustration on Stellar Tracks D. Fraix-Burnet1, M. Thuillard2 1 Univ. Grenoble Alpes, CNRS, IPAG, 38000 Grenoble, France email: [email protected] 2 La Colline, 2072 St-Blaise, Switzerland February 7, 2018 This pedagogicalarticle was written in 2014 and is yet unpublished. Partofit canbefoundin Fraix-Burnet (2015). Abstract Classifying objects into groups is a natural activity which is most often a prerequisite before any physical analysis of the data. Clustering and phylogenetic approaches are two different and comple- mentary ways in this purpose: the first one relies on similarities and the second one on relationships. In this paper, we describe very simply these approaches and show how phylogenetic techniques can be used in astrophysics by using a toy example based on a sample of stars obtained from models of stellar evolution.
    [Show full text]
  • Molecular Phylogenetics: Principles and Practice
    REVIEWS STUDY DESIGNS Molecular phylogenetics: principles and practice Ziheng Yang1,2 and Bruce Rannala1,3 Abstract | Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use. statistical Systematics Before the advent of DNA sequencing technologies, phylogenetics, creating the emerging field of 2,18,19 The inference of phylogenetic phylogenetic trees were used almost exclusively to phylogeography. In species tree methods , the gene relationships among species describe relationships among species in systematics and trees at individual loci may not be of direct interest and and the use of such information taxonomy. Today, phylogenies are used in almost every may be in conflict with the species tree. By averaging to classify species. branch of biology. Besides representing the relation- over the unobserved gene trees under the multi-species 20 Taxonomy ships among species on the tree of life, phylogenies
    [Show full text]
  • Ecdysozoan Phylogeny and Bayesian Inference: First Use of Nearly Complete 28S and 18S Rrna Gene Sequences to Classify the Arthro
    MOLECULAR PHYLOGENETICS AND EVOLUTION Molecular Phylogenetics and Evolution 31 (2004) 178–191 www.elsevier.com/locate/ympev Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kinq Jon M. Mallatt,a,* James R. Garey,b and Jeffrey W. Shultzc a School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA b Department of Biology, University of South Florida, 4202 East Fowler Ave. SCA110, Tampa, FL 33620, USA c Department of Entomology, University of Maryland, College Park, MD 20742, USA Received 4 March 2003; revised 18 July 2003 Abstract Relationships among the ecdysozoans, or molting animals, have been difficult to resolve. Here, we use nearly complete 28S + 18S ribosomal RNA gene sequences to estimate the relations of 35 ecdysozoan taxa, including newly obtained 28S sequences from 25 of these. The tree-building algorithms were likelihood-based Bayesian inference and minimum-evolution analysis of LogDet-trans- formed distances, and hypotheses were tested wth parametric bootstrapping. Better taxonomic resolution and recovery of estab- lished taxa were obtained here, especially with Bayesian inference, than in previous parsimony-based studies that used 18S rRNA sequences (or 18S plus small parts of 28S). In our gene trees, priapulan worms represent the basal ecdysozoans, followed by ne- matomorphs, or nematomorphs plus nematodes, followed by Panarthropoda. Panarthropoda was monophyletic with high support, although the relationships among its three phyla (arthropods, onychophorans, tardigrades) remain uncertain. The four groups of arthropods—hexapods (insects and related forms), crustaceans, chelicerates (spiders, scorpions, horseshoe crabs), and myriapods (centipedes, millipedes, and relatives)—formed two well-supported clades: Hexapoda in a paraphyletic crustacea (Pancrustacea), and ÔChelicerata + MyriapodaÕ (a clade that we name ÔParadoxopodaÕ).
    [Show full text]
  • Procedures for the Analysis of Comparative'data Using Phylogenetically Independent Contrasts
    PROCEDURES FOR THE ANALYSIS OF COMPARATIVE'DATA USING PHYLOGENETICALLY INDEPENDENT CONTRASTS THEODOREGARLAND, JR.,' PAULH. HARVEY?AND ANTHONYR. IVES' 'Department of Zoology, University of Wisconsin, Madison, Wisconsin 53706, USA 2Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, England Abstract.-We discuss and clarify several aspects of applying Felsenstein's (1985, Am. Nat. 125: 1-15) procedures to test for correlated evolution of continuous traits. This is one of several available comparative methods that maps data for phenotypic traits onto an existing phylogenetic tree (derived from independent information). Application of Felsenstein's method does not require an entirely dichotomous topology. It also does not require an assumption of gradual, clocklike character evolution, as might be modeled by Brownian motion. Almost any available information can be used to estimate branch lengths (e.g., genetic distances, divergence times estimated from the fossil record or from molecular clocks, numbers of character changes from a cladistic analysis). However, the adequacy for statistical purposes of any proposed branch lengths must be verified empirically for each phylogeny and for each character. We suggest a simple way of doing this, based on graphical analysis of plots of standardized independent contrasts versus their standard deviations (i.e., the square roots of the sums of their branch lengths). In some cases, the branch lengths and/or the values of traits being studied will require transformation. An example involving the scaling of mammalian home range area is presented. Once adequately standardized, sets of independent contrasts can be analyzed using either linear or nonlinear (multiple) regression. In all cases, however, regressions (or correlations) must be computed through the origin.
    [Show full text]
  • Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2006-12-01 Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation Ashley N. Egan Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Egan, Ashley N., "Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation" (2006). Theses and Dissertations. 1294. https://scholarsarchive.byu.edu/etd/1294 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. by Brigham Young University in partial fulfillment of the requirements for the degree of Brigham Young University All Rights Reserved BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL and by majority vote has been found to be satisfactory. ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the format, citations and
    [Show full text]
  • The Minimum-Evolution Distance-Based Approach to Phylogeny Inference Richard Desper, Olivier Gascuel
    The Minimum-Evolution Distance-Based Approach to Phylogeny Inference Richard Desper, Olivier Gascuel To cite this version: Richard Desper, Olivier Gascuel. The Minimum-Evolution Distance-Based Approach to Phylogeny Inference. O. Gascuel. Mathematics of Evolution and Phylogeny, Oxford University Press, pp.1-32, 2005, 0-19-856610-7. lirmm-00106579 HAL Id: lirmm-00106579 https://hal-lirmm.ccsd.cnrs.fr/lirmm-00106579 Submitted on 13 May 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 1 THE MINIMUM EVOLUTION DISTANCE-BASED APPROACH TO PHYLOGENETIC INFERENCE Richard Desper and Olivier Gascuel Distance algorithms remain among the most popular for reconstructing phylogenies, especially for researchers faced with data sets with large num- bers of taxa. Distance algorithms are much faster in practice than character or likelihood algorithms, and least-squares algorithms produce trees that have several desirable statistical properties. The fast Neighbor Joining heuristic has proven to be quite popular with researchers, but suffers some- what from a lack of a statistical foundation. We show here that the balanced minimum evolution approach provides a robust statistical justification and is amenable to fast heuristics that provide topologies superior among the class of distance algorithms.
    [Show full text]
  • Phylogenetic Analyses: Comparing Species to Infer Adaptations and Physiological Mechanisms Enrico L
    P1: OTA/XYZ P2: ABC JWBT335-c100079 JWBT335/Comprehensive Physiology November 1, 2011 18:56 Printer Name: Yet to Come Phylogenetic Analyses: Comparing Species to Infer Adaptations and Physiological Mechanisms Enrico L. Rezende*1 and Jose´ Alexandre F. Diniz-Filho2 ABSTRACT Comparisons among species have been a standard tool in animal physiology to understand how organisms function and adapt to their surrounding environment. During the last two decades, conceptual and methodological advances from different fields, including evolutionary biology and systematics, have revolutionized the way comparative analyses are performed, resulting in the advent of modern phylogenetic statistical methods. This development stems from the realiza- tion that conventional analytical methods assume that observations are statistically independent, which is not the case for comparative data because species often resemble each other due to shared ancestry. By taking evolutionary history explicitly into consideration, phylogenetic statistical methods can account for the confounding effects of shared ancestry in interspecific comparisons, improving the reliability of standard approaches such as regressions or correlations in compara- tive analyses. Importantly, these methods have also enabled researchers to address entirely new evolutionary questions, such as the historical sequence of events that resulted in current patterns of form and function, which can only be studied with a phylogenetic perspective. Here, we pro- vide an overview of phylogenetic approaches and their importance for studying the evolution of physiological processes and mechanisms. We discuss the conceptual framework underlying these methods, and explain when and how phylogenetic information should be employed. We then outline the difficulties and limitations inherent to comparative approaches and discuss po- tential problems researchers may encounter when designing a comparative study.
    [Show full text]
  • Basics for the Construction of Phylogenetic Trees
    Article ID: WMC002563 ISSN 2046-1690 Basics for the Construction of Phylogenetic Trees Corresponding Author: Mr. B P Niranjan Reddy, Senior Research Fellow, School of Sciences in Biotechnology, Jiwaji University - India Submitting Author: Mr. B.P.Niranjan Reddy, Senior Research Fellow, School of Sciences in Biotechnology, Jiwaji University - India Article ID: WMC002563 Article Type: Review articles Submitted on:03-Dec-2011, 11:47:15 AM GMT Published on: 03-Dec-2011, 08:06:40 PM GMT Article URL: http://www.webmedcentral.com/article_view/2563 Subject Categories:BIOLOGY Keywords:Phylogenetic tree, Model selection, Bootstrapping, Phylogeny free software How to cite the article:Niranjan Reddy B P. Basics for the Construction of Phylogenetic Trees . WebmedCentral BIOLOGY 2011;2(12):WMC002563 Source(s) of Funding: None Competing Interests: None Additional Files: Links to some very useful web pages for phylogenet WebmedCentral > Review articles Page 1 of 11 WMC002563 Downloaded from http://www.webmedcentral.com on 05-Dec-2011, 05:19:58 AM Basics for the Construction of Phylogenetic Trees Author(s): Niranjan Reddy B P Abstract the genes into various classes like orthologs, paralogs, in- or out-paralogs, to understand the evolution of the new functions through duplications, horizontal gene transfers, gene conversion, recombination, and Phylogeny- A Diagram for Evolutionary Network-is co-evolution etc. (Hafner and Nadler, 1988; Nei, 2003; used to infer the phylogenetic relationships among the Pagel, 2000). Phylogenetic analysis provides a species or genes. The phylogenetic analysis including powerful tool for comparative genomics (Pagel, 2000). morphological, biological, and bionomic characters, Genome sequencing projects are providing valuable allozyme, RFLP data have been extensively used to sequence information that is widely used to infer the infer the evolutionary relationship among the species evolutionary relationship between different species or during the pre-genomic era.
    [Show full text]
  • Rapid Speciation and Ecological Divergence in the American Seven-Spined Gobies (Gobiidae, Gobiosomatini) Inferred from a Molecular Phylogeny
    Evolution, 57(7), 2003, pp. 1584±1598 RAPID SPECIATION AND ECOLOGICAL DIVERGENCE IN THE AMERICAN SEVEN-SPINED GOBIES (GOBIIDAE, GOBIOSOMATINI) INFERRED FROM A MOLECULAR PHYLOGENY LUKAS RUÈ BER,1,2 JAMES L. VAN TASSELL,3,4 AND RAFAEL ZARDOYA1,5 1Departamento de Biodiversidad y BiologõÂa Evolutiva, Museo Nacional de Ciencias Naturales, Jose GutieÂrrez Abascal 2, 28006 Madrid, Spain 2E-mail: [email protected] 3Department of Biology, Hofstra University, Hempstead, New York 11549 4E-mail: [email protected] 5E-mail: [email protected] Abstract. The American seven-spined gobies (Gobiidae, Gobiosomatini) are highly diverse both in morphology and ecology with many endemics in the Caribbean region. We have reconstructed a molecular phylogeny of 54 Gobio- somatini taxa (65 individuals) based on a 1646-bp region that includes the mitochondrial 12S rRNA, tRNA-Val, and 16S rRNA genes. Our results support the monophyly of the seven-spined gobies and are in agreement with the existence of two major groups within the tribe, the Gobiosoma group and the Microgobius group. However, they reject the monophyly of some of the Gobiosomatini genera. We use the molecular phylogeny to study the dynamics of speciation in the Gobiosomatini by testing for departures from the constant speciation rate model. We observe a burst of speciation in the early evolutionary history of the group and a subsequent slowdown. Our results show a split among clades into coastal-estuarian, deep ocean, and tropical reef habitats. Major habitat shifts account for the early signi®cant accel- eration in lineage splitting and speciation rate and the initial divergence of the main Gobiosomatini clades.
    [Show full text]