Upload File

a comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions...

  • Home
  • Documents
  • A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics
prev
next
out of 17
Download A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

Upload: wilso04

Post on 07-Apr-2018

228 views

Category:

Documents


0 download

Report

TRANSCRIPT

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    1/17

    A Comparison of

    Practicality,Phylogenetic Utility

    and Phylogenetic Signal of

    Priority Gene RegionsRecommended for

    Lepidoptera Phylogenetics

    By John James Wilson

    University of Guelph

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    2/17

    The "Tower of Babel" in

    Lepidoptera systematics

    The Tower of Babel by Pieter Brueghel the Elder (1563).

    Introduction Methods Results Discussion

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    3/17

    OBJECTIVES

    Introduction Methods Results Discussion

    Develop methods to quantify and compare

    the priority gene regions designated for

    Lepidoptera molecular systematics

    Determine if these genes are acceptable

    Particularly see how the DNA barcode

    segment of COI compares to nuclear genes at

    different levels of the taxonomic hierarchy

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    4/17

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    5/17

    Practicality

    a) Universality of primers

    b) Quality of sequences

    CodonCode Aligner www.codoncode.com

    Introduction Methods Results Discussion

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    6/17

    Phylogenetic Utility

    Systematic

    Entomology

    2009

    Measured prior to phylogenetic analysis

    a)Number of characters variable, informative

    b)Genetic distances~ 6750 bp total

    Introduction Methods Results Discussion

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    7/17

    Phylogenetic Signal

    The tendency for related species to resembleeach other (www.nature.com)

    Ability of the characters to group phylogeneticallyrelated taxa together

    Measured after phylogenetic analysis

    a) Within the dataset (homoplasy)b)Through congruence with other (independent)

    types of data

    Introduction Methods Results Discussion

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    8/17

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    9/17

    Introduction Methods Results Discussion

    Phylogenetic utility

    -Sequences aligned in BIOEDIT

    -Number of character calculated in PAUP

    -Pairwise phenetic distances calculated in MEGA

    977 species available from GenBank with sequences for 3 genes

    COI (barcode fragment), EF1a, WG

    ~20 families

    ~200 genera

    Taxon sampling

    Phylogenetic signal-Cladogram constructed in PAUP

    -14 family-level tests of monophyly

    -109 genus-level tests of monophyly

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    10/17

    Introduction Methods Results Discussion

    1. Proportion of monophyletic taxa# of monophyletic taxa/number of taxa

    2. Taxon consistency index = m/s

    m = minimum # of clades a taxon can exhibit on any

    cladogram

    s = minimum # of clades a taxon exhibits on actual

    cladogram

    3. Taxon retention index = (g-s)/(g-m)g = greatest # of clades a taxon can exhibit on any

    cladogram

    Phylogenetic signal

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    11/17

    RiodinidaePieridae

    HesperiidaeNymphalidaeLycaenidae

    Geometridae

    Hedylidae

    SematuridaeUraniidae

    Noctuidae

    Sphingidae

    Saturniidae

    Papilionidae

    Notodontidae

    Bombycidae

    Lymantriidae

    Pyralidae

    Arctiidae

    Immidae

    Crambidae

    Lasiocampidae

    Mimallonidae

    Thyridae

    Hyblaeidae

    Introduction Methods Results Discussion

    COI

    EF1a WG 18S CAD DDC

    Practicality

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    12/17

    RiodinidaePieridae

    HesperiidaeNymphalidaeLycaenidae

    Geometridae

    Hedylidae

    SematuridaeUraniidae

    Noctuidae

    Sphingidae

    Saturniidae

    Papilionidae

    Notodontidae

    Bombycidae

    Lymantriidae

    Pyralidae

    Arctiidae

    Immidae

    Crambidae

    Lasiocampidae

    Mimallonidae

    Thyridae

    Hyblaeidae

    Introduction Methods Results Discussion

    COI

    EF1a WG 18S CAD DDC

    Practicality

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    13/17

    Introduction Methods Results Discussion

    Phylogenetic utility

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    14/17

    Introduction Methods Results Discussion

    Phylogenetic utility

    COI

    EF1a

    WG

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    15/17

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    16/17

    Introduction Methods Results Discussion

    Practicality

    a) Universality of primers: COI >WG >EF1a

    b) Quality of sequences: COI >WG >EF1a

    Phylogenetic utility

    a) Informative characters: WG >COI >EF1a

    b) Phenetic distance: WG >COI >EF1a

    Phylogenetic signal

    a)Homoplasy: WG >EF1a >COI

    b)Congruence: Family: WG >EF1a >COI

    Genus: WG >COI> EF1a

    LIFE IS A TRADE-OFF

  • 8/6/2019 A comparison of practicality, phylogenetic utility and phylogenetic signal of priority gene regions recommended for Lepidoptera phylogenetics

    17/17

    Funding & Support

    Joo Lima

    Listed on the Canadian Centre for DNA Barcoding

    website:www.dnabarcoding.ca

    Area de Conservacin

    Guanacaste

    Dan Janzen, Winnie Hallwachs & ACG

    Parataxonomists

    Laboratory


Molecular Phylogenetics and Evolution · 582 D. Zuccon et al./Molecular Phylogenetics and Evolution 62 (2012) 581–596 Table 1 Samples and sequences included in the phylogenetic

Molecular Phylogenetics and Evolutionpeople.oregonstate.edu/~weisv/assets/18sprolesetal.pdf · uptake. Homologous protein sequences were used for phylogenetic analysis and tertiary

ComplimentaryContributorCopy - ATSPACEacacia.atspace.eu/papers/Networks3.pdf2. Phylogenetics 2.1. Phylogenetic Analysis The study of evolutionary processes has often been considered

Phylogenetics. Phylogenetic Trees time NODE BRANCH ROOT Operational Taxonomic Unit (OTU) Hypothetical Taxonomic Unit

Molecular Phylogenetics and Evolution · The phylogenetic relationships and generic limits of finches (Fringillidae) Dario Zuccona,⇑, Robert Pryˆs-Jonesb, Pamela C. Rasmussenc,

Mar 2004 Irit Orr Phylogenetic Analysis Introduction to · Phylogenetic Analysis Irit Orr Mar 2004 Subjects of this lecture 1 Introducing some of the terminology of phylogenetics

Molecular Phylogenetics and Evolution - WordPress.com · 2.3. Phylogenetic analyses Sequences were aligned with Se-Al v.2.0a11 (Rambaut, 2002). Phylogenetic trees of individual and

Introduction to Phylogenetics. Phylogenetics Phylogenetics is the study of evolutionary relationships among a group of organisms. Phylogenetic analysis

Phylogenetics Phylogenetic trees illustrate the evolutionary relationships among groups of organisms, or among a family of related nucleic acid or protein

CS 177 Phylogenetics I Taxonomy and phylogenetics Phylogenetic trees Cladistic versus phenetic analyses Model of sequence evolution Phylogenetic trees

Phylogenetics and Biodiversity Philadelphia, Pennsylvania, 17-18 April 2015 “Can phylogenetic diversity be the basis for a planetary boundary for biodiversity?”

Introduction to phylogenetics using · Limitations: computer-intensive, model selection possibly cumbersome. The software implements one of the largest selections of phylogenetic

Stat 882: Statistical Phylogenetics – Lecture 11 Introduction 1.1 Phylogenetic Trees What is phylogenetics? • Phylogenetics = the study of the evolutionary relationships among

Molecular Phylogenetics and Evolutiond284f45nftegze.cloudfront.net/clinnen/Linnen_Farrell_2008mpe.pdf · Phylogenetic analysis of nuclear and mitochondrial genes reveals evolutionary

Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Lecture #6 Page 1 Week6: Intro to Phylogenetic Reconstruction

Molecular Phylogenetics and Evolution · recognized through molecular phylogenetic analysis. Initial indications of these relationships came from phylogenies based on ribosomal RNA

MOLECULAR PHYLOGENETICS Four main families of molecular phylogenetic methods : Parsimony Distance methods Maximum likelihood methods Bayesian methods

1 Dendroscope – An interactive viewer for large phylogenetic trees Daniel H. Huson Phylogenetics Programme, Newton Institute, September 2007 - and networks

Coalescent Theory: An Introduction for Phylogenetics · Population Genetics Models Coalescent Theory for Phylogenetic Inference Why study population genetics? Wright-Fisher Model

Phylogenetic analysis is an inference of evolutionary relationships between organisms. Phylogenetics tries to answer the question “How did groups of organisms

1 General Phylogenetics Points that will be covered in this presentation Tree TerminologyTree Terminology General Points About Phylogenetic TreesGeneral

Molecular Phylogenetics and Evolutionecoevo.com.br/publicacoes/pesquisadores/maria_jose/2014 Machad… · Phylogenetic relationships within Bothrops neuwiedi group (Serpentes, Squamata):

AP Bio Review Day 3 Agenda: 1.Phylogenetics and Evolution 2. Osmosis and Transport 3. Phylogenetic Worksheets 4. Exit Ticket

How do we infer phylogeny? 3 “schools” of phylogenetic thought: 1.Evolutionary systematics 1.Phenetics 1.Cladistics/phylogenetics

2016-30 Molecular Phylogenetics and Evolution: 94(2016)A ... · 2016-30 Molecular Phylogenetics and Evolution: 94(2016)A: 242-251 Phylogenetic relationships and evolutionary history

A primer to phylogenetic analysis using the PHYLIP package · intented to be a course in phylogenetics, although some phylogenetic concepts will be discussed briefly. There are other

What is a synapomorphy?. Terms systematics [taxonomy, phylogenetics] phylogeny/phylogenetic tree cladogram tips, branches, nodes homology apomorphy synapomorhy

Molecular Phylogenetics and Evolutiondonoghuelab.yale.edu/sites/default/files/209_lo...Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae)

Phylogenetic Inference and Hypothesis Testing - …laic/testing.pdf · 2005-09-27 · Phylogenetic Inference and Hypothesis Testing Catherine Lai (92720) BSc ... 4 Phylogenetics Tree

Phylogenetic Analysis – Part I Spring 2014. Outline Systematics Phenetics (brief review) Phylogenetics & Characters Evolutionary Trees

Molecular Phylogenetics (Hannes Luz)Molecular Phylogenetics (Hannes Luz) Contents: •Phylogenetic Trees, basic notions •A character based method: Maximum Parsimony •Trees from

Package ‘ape’ape-package Analyses of Phylogenetics and Evolution Description ape provides functions for reading, writing, manipulating, analysing, and simulating phylogenetic trees

Biology Essentials - 006waterworthapbiology.weebly.com/uploads/2/2/2/1/...Biology Essentials - 006 bozemanscience.com. Phylogenetics Phylogenetic! Tree Cladogram Speciation Morphological

Chapter 5 Molecular phylogenetics and taxonomic reassessment …shodhganga.inflibnet.ac.in/bitstream/10603/5275/10/10_chapter 5.pdf · adopting a phylogenetic-based approach. This

Targeted Enrichment of Large Gene Families for Phylogenetic ...edwardslab.org/reprints/moore_etal_sysbio2018.pdfspeciation events), these loci would be especially useful for phylogenetics;