Plant Phylogenomics: Lessons from the 1KP Project!
|
|
|
- Baldric Sparks
- 6 years ago
- Views:
Transcription
1 Plant Phylogenomics: Lessons from the 1KP Project! Jim Leebens-Mack! Department of Plant Biology! University of Georgia! New Methods for Phylogenomics and Metagenomics Symposium! Feb, 2013!
2 Ancestral Angiosperm/! Amborella Genome! Vic Albert! Raj Ayyampalayam! Brad Barbazuk! John Bowers! Jim Burnette! Srikar Chamala! Andre Chanderbali! Josh Der! Claude depamphils! Jamie Estill! Hong Ma! Doug & Pam Soltis! Stephan Schuster! Sue Wessler! Rod Wing! Kerr Wall! Norm Wickett! Eric Wafula! Collaborators! MonAToL! Claude depamphilis! Tom Givnish! Cecile Ané! Raj Ayyampalayam! Sean Graham! Dennis Stevenson! Jerry Davis! Alejandra Gandolfo! Chris Pires! Norm Wickett! Wendy Zomlefer! Michael McKain! Jill Duarte! Funding: NSF, iplant, University of Georgia, OneKP OneKP/MSA AToL! Norman Wickett! Nam Nguyen! Siavash Mirarab! Naim Mataci! Gane Ka-Shu Wong! BGI! Eric Carpenter! Brad Ruhfel! Herve Philippe.! Gordon Burleigh! Matt Barker! Claude depamphilis! Tandy Warnow! Jamie Estill! Raj Ayyampalayam! Doug & Pam Soltis! Sean Graham! Dennis Stevenson! Michael Melkonian! OneKP Consortium!
3 Nothing in biology makes sense except in the light of evolution (Theodosius Dobzhansky, 1973)! Nothing in evolution makes sense except in the light of phylogeny! Darwin (1837) First Notebook on Transmutation of Species!
4 Phylogenomics - Jonathan Eisen (1998; Genome Research 8: )!
5 Current Usages! 1. Using genome-scale data to resolve phylogentic relationships! 2. Genome-Scale comparisons placed within a phylogenetic context!
6 Phylogenomics 1 : Plastid Genome Phylogeny Resolving Many Previously Intractable Questions in Plant Systematics! Liriodendron tulipifera 159,885 bp Jansen et al PNAS!
7 What About Nuclear Gene Histories?! Gane Ka Shu Wong (Alberta) ancangio.uga.edu monatol.uga.edu iplant Tree of Life
8 Phylo-Transcriptomics! Ambore lla Liriodendr on2 Liriodendr on1 Pers ea Saru ma Horde um Triticu m Oryz azea mays Sorgh um Sacchar um Asparag us1 Asparag us2 Alliu m Yucc a Medica go Lotu s Glyci nepopulus trichocarpa Populus tremuloides Ros a Arabidop sis Descurai nia Gossypi um Viti s Suae da Solanu m Solanum lycopersicon Solanum hirsutum
9 Gene Family Circumscription, Sequence Alignment, Gene Tree Estimation and Species Tree Estimation! Reference Proteomes +! New Transcriptome! Data! Full-Length Coding Sequence Database (Sequenced Genomes, Refseq ) MCL-based Gene Family Circumscription! Coding Sequence Databases for each Species (Transcriptome Assemblies)! SATe Multiple-sequence Alignment! Gene Tree Estimation! Core Gene Family Scaffolds! HMM Estimation! for each Gene Family! Gene Family HMMs! HMM Sorting of! Coding Sequences! Into Gene Families! Gene Family Fasta Files! SuperTree Analysis! (Burleigh & Eulenstein)! SuperMatrix Analysis! (desalle et al. [AMNH])! Species Tree Estimation Low Copy Gene SuperMatrix Analysis! (depamphilis et al.)!
10 Gene Family Classification for Full-Length Genes from Sequenced Genomes orthomcl clustering!
11 Gain and Loss of Gene Families! 1000 GF clusters! Large increases! on internal branches! rosids! asterids! monocots! eudicots! Angiosperms!
12 angiosperms gymnosperms eudicots monocots ferns magnoliids rosids commelinids basal eudicots asterids conifers hornworts green algae liverworts chlorophytes mosses charophytes 1kP 1,000,000 gene width scalebar NCBI
13 1kp Questions to be Addressed through Estimation of Gene Trees and Species Relationships! What are the relationships among lineages across the green plant tree of life?! What was the nature and gene composition of the likely ancestor of the Viridiplantae?! What was the impact of lateral gene transfer (from bacteria) on the early evolution of the Viridiplantae and the Chlorophyta/ Streptophytra?! Were gene and/or genome duplication events associated with innovations in green plant evolution including the origin of the flower, the seed, the vascular cambium (wood), alternation of generations, the shift from a life history dominated by the haploid phase to a dominant diploid life stage, colonization of land and shifts from single cells to multicellularity,! Has polyploidy played a role in the diversification of angiosperms?!
14 Check out OneKP data!
15 Surprises from Phylogenomics: Monophyly of Conifers?! Plastid Genome Analyses! Large Nuclear Gene Analyses! double fertilization porose vessels Cibrián et al. 2010, Lee et al 2011, OneKp unpublished!
16 Origin of Land Plants: Retention of egg, phragmoplast and plasmodesmata preadaptations for colonization of land! Green Plants (Viridophytes) [Fossil groups] Coleochaete! Charales! sporangium gametangia retenlon of egg, phragmoplast and plasmodesmata Age ~1.5 billion years filamentous growth cell plate cell wall
17 Plastid phylogenomic analyses yielding surprising results for the origin of land plants filamentous rather than more complex algal lineages inferred sister to Land Plants!! Land Plants ML MP ML-distance LogDet-distance Chara vulgaris cp genome 184,933 bp Monique Turmel et al 2006 MBE!
18 Loss! Land Plants retenlon of egg, phragmoplast and plasmodesmata Analysis of 604 single-copy nuclear genes agrees with plastome analysis suggesting that retention of egg, plasmodesmata, and phragmoplast lost in diverse Zygnemophyceae!
19 Why should you believe these results?! You shouldn t. Inferred trees are hypotheses!
20 Consider Possible Complications! Lots of missing data!! Remove genes/taxa with lots of missing data! Ortholog identification! Focus on genes/genomes that tend not to be duplicated! Contamination! BLAST, Sequence placement on reference tree (SEPP?), Long branch trimming! Model misspecification! Model validation simulations! Test robustness of hypothesis among inferences derived from alternative models!
21 Contamination is an issue!
22 Data Matrix/Analysis Perturbation! DNA vs Amino Acids! All codon positions vs remove third position! Remove gappy genes or sites! Remove genes on long branches in gene trees! Remove genes where contamination seems to persist.! Supermatrix and Supertree estimation!
23 Good News: Some results seem to be very robust!
24 Issues with inclusion of 3 rd codon position?! Amino Acids! 1 st & 2 nd! Codon Pos! Supertree! AA/1 st 2 nd All Pos! All Codon! Pos!
25 Problems due to heterogeneous substitution process?!
26 Filamentous Algae + Land Plant Hypothesis Seems to be Robust! Amino Acids! 1 st & 2 nd! Codon Pos! Supertree! AA/1 st 2 nd!
27 Land Plants retenlon of egg, phragmoplast and plasmodesmata Loss!
28 Supertree and Supermatrix Analyses Provide Different Inferences Concerning the Monophyly of Conifers! Amino Acids! 1 st & 2 nd! Codon Pos! Supertree! AA/1 st 2 nd!
29 Mosses Sister + Liverworts Clade Sister to Vascular Plants?! Amino Acids! 1 st & 2 nd! Codon Pos! Supertree! AA/1 st 2 nd!
30 Conclusions! Genome-scale phylogenetic inference is complex! Model mis-specification can results in statistical inconsistency: more data -> stronger support for the wrong answer.! Proposal: Apply multiple analysis strategies and explore/understand basis of conflicts among resulting trees!
31 Phylogenomics???! 1. Using genome-scale data to resolve phylogentic relationships! 2. Genome-Scale comparisons placed in a phylogenetic context!
32 Phylogenetic Analysis and Molecular Dating of 100 s of Gene Families Implicates Genome Duplications Associated with Origin of Angiosperms and Seed Plants! Jiao et al. 2011!
33 Thank You!!
Using Ensembles of Hidden Markov Models for Grand Challenges in Bioinformatics
Using Ensembles of Hidden Markov Models for Grand Challenges in Bioinformatics Tandy Warnow Founder Professor of Engineering The University of Illinois at Urbana-Champaign http://tandy.cs.illinois.edu
Major lineages and life cycles of land plants. Green plants: viridiplantae
Liverworts Mosses Hornworts Lycophytes Major lineages and life cycles of land plants Green plants: viridiplantae Green plants Embryophytes (land plants) Bryophytes Tracheophytes (vascular plants) Seed
Diversity of Plants How Plants Colonized the Land
Chapter 29, 30. Diversity of Plants How Plants Colonized the Land 1 The first plants For more than 3 billion years, Earth s terrestrial surface was lifeless life evolved in the seas 1st photosynthetic
How to detect paleoploidy?
Genome duplications (polyploidy) / ancient genome duplications (paleopolyploidy) How to detect paleoploidy? e.g. a diploid cell undergoes failed meiosis, producing diploid gametes, which selffertilize
Kingdom: Plantae. Domain Archaea. Domain Eukarya. Domain Bacteria. Common ancestor
Kingdom: Plantae Domain Eukarya Domain Bacteria Domain Archaea Domain Eukarya Common ancestor The First Plants For more than 3 billion years, Earth s terrestrial surface was lifeless life evolved in the
Plant Evolution & Diversity
Plant Evolution & Diversity Ancestors of plants were probably charophytes (green algae) Chlorophyll a and b, beta carotene Similar thylakoid arrangements Identical cell walls Starch as a storage carbohydrate
Phylogenomics, Multiple Sequence Alignment, and Metagenomics. Tandy Warnow University of Illinois at Urbana-Champaign
Phylogenomics, Multiple Sequence Alignment, and Metagenomics Tandy Warnow University of Illinois at Urbana-Champaign Phylogeny (evolutionary tree) Orangutan Gorilla Chimpanzee Human From the Tree of the
1 Mosses and other bryophytes are like ferns in that both bryophytes and ferns exhibit each of the following traits EXCEPT
Page 1 1 Mosses and other bryophytes are like ferns in that both bryophytes and ferns exhibit each of the following traits EXCEPT A haploid spores. B specialized cells and tissues. C vascular tissue for
CHAPTER 29 PLANT DIVERSITY I: HOW PLANTS COLONIZED LAND. Section A: An Overview of Land Plant Evolution
CHAPTER 29 PLANT DIVERSITY I: HOW PLANTS COLONIZED LAND Section A: An Overview of Land Plant Evolution 1. Evolutionary adaptations to terrestrial living characterize the four main groups of land plants
Reproductive Morphology
Week 3; Wednesday Announcements: 1 st lab quiz TODAY Reproductive Morphology Reproductive morphology - any portion of a plant that is involved with or a direct product of sexual reproduction Example: cones,
Ms.Sastry, AP Biology Unit 4/Chp 26 to 34/Diversity 1 Chapter in class follow along lecture notes
Ms.Sastry, AP Biology Unit 4/Chp 26 to 34/Diversity 1 Chapter 26 34 in class follow along lecture notes Chp 26 Origin of life: 1) When did earth form? 2) What is the order of evolution of life forms on
Cladistics and Bioinformatics Questions 2013
AP Biology Name Cladistics and Bioinformatics Questions 2013 1. The following table shows the percentage similarity in sequences of nucleotides from a homologous gene derived from five different species
Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline
Phylogenetics Todd Vision iology 522 March 26, 2007 pplications of phylogenetics Studying organismal or biogeographic history Systematics ating events in the fossil record onservation biology Studying
Chapter 29: Plant Diversity I How Plants Colonized Land
Chapter 29: Plant Diversity I How Plants Colonized Land 1. Evolutionary History of Plants 2. General Features of Plants 3. Survey of the Plant Kingdom A. Nonvascular Plants B. Seedless Vascular Plants
Origins of Life. Fundamental Properties of Life. Conditions on Early Earth. Evolution of Cells. The Tree of Life
The Tree of Life Chapter 26 Origins of Life The Earth formed as a hot mass of molten rock about 4.5 billion years ago (BYA) -As it cooled, chemically-rich oceans were formed from water condensation Life
Evolutionary model for the statistical divergence of paralogous and orthologous gene pairs generated by whole genome duplication and speciation
Zhang et al. RESEARCH Evolutionary model for the statistical divergence of paralogous and orthologous gene pairs generated by whole genome duplication and speciation Yue Zhang, Chunfang Zheng and David
Big Questions. Is polyploidy an evolutionary dead-end? If so, why are all plants the products of multiple polyploidization events?
Plant of the Day Cyperus esculentus - Cyperaceae Chufa (tigernut) 8,000 kg/ha, 720 kcal/sq m per month Top Crop for kcal productivity! One of the world s worst weeds Big Questions Is polyploidy an evolutionary
Impact of recurrent gene duplication on adaptation of plant genomes
Impact of recurrent gene duplication on adaptation of plant genomes Iris Fischer, Jacques Dainat, Vincent Ranwez, Sylvain Glémin, Jacques David, Jean-François Dufayard, Nathalie Chantret Plant Genomes
Chapter 29 Plant Diversity I: How Plants Colonized Land
Chapter 29: Plant Diversity I: How Plants Colonized Land Chapter 29 Plant Diversity I: How Plants Colonized Land Name Period Concept 29.1 Land plants evolved from green algae 1. Plants colonized land about
8/23/2014. Phylogeny and the Tree of Life
Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major
Chapter 26: Phylogeny and the Tree of Life Phylogenies Show Evolutionary Relationships
Chapter 26: Phylogeny and the Tree of Life You Must Know The taxonomic categories and how they indicate relatedness. How systematics is used to develop phylogenetic trees. How to construct a phylogenetic
-plant bodies composed of tissues produced by an apical meristem. -spores with tough walls. -life history of alternation of generations
Chapter 21-Seedless Plants Major modern plant groups All groups of land-adapted plants have a common set of characteristics: -plant bodies composed of tissues produced by an apical meristem -spores with
Some History: In the life cycle of the kelp Laminaria. One way to separate algae from protozoa is that. Rocks of Cambrian Age (ca.
One way to separate algae from protozoa is that a. Protozoa are photosynthetic, while algae are not. b. Algae are photosynthetic, while protozoa are not. c. Protozoa are prokaryotic, while algae are eukaryotic.
Botany: Part I Overview of Plants & Plant Structure
Botany: Part I Overview of Plants & Plant Structure Plant evolution Plant Evolution Chlorophytes Bryophytes (nonvascular plants) Seedless vascular plants Gymnosperms Angiosperms Chlorophytes are a green
LAB 4: PHYLOGENIES & MAPPING TRAITS
LAB 4: PHYLOGENIES & MAPPING TRAITS *This is a good day to check your Physcomitrella (protonema, buds, gametophores?) and Ceratopteris cultures (embryos, young sporophytes?)* Phylogeny Introduction The
AP Biology. Evolution of Land Plants. Kingdom: Plants. Plant Diversity. Animal vs. Plant life cycle. Bryophytes: mosses & liverworts
Kingdom: Plants Domain Eukarya Domain Domain Domain Eubacteria Archaea Eukarya 2007-2008 Common ancestor Evolution of Land Plants 500 mya land plants evolved special adaptations for life on dry land protection
MiGA: The Microbial Genome Atlas
December 12 th 2017 MiGA: The Microbial Genome Atlas Jim Cole Center for Microbial Ecology Dept. of Plant, Soil & Microbial Sciences Michigan State University East Lansing, Michigan U.S.A. Where I m From
Plants Review 1. List the 6 general characteristics of plants. 2. What did plants probably evolve from? 3. What are some advantages for life on land
Plants Review 1. List the 6 general characteristics of plants. 2. What did plants probably evolve from? 3. What are some advantages for life on land for a plant? 4. What are the 3 main groups of plants?
Plant Evolution and Diversity. B. Importance of plants. C. Where do plants fit, evolutionarily? What are the defining traits of plants?
Plant Evolution and Diversity Reading: Chap. 30 I. What is a plant? A. Basic structure and function B. Why are plants important? C. What are plants, evolutionarily? D. Problems of living on land II. Overview
EDUCATION: PhD Ecology and Evolutionary Biology, University of Connecticut 2007 BSc Biology (Botany), University of British Columbia 2001
CURRICULUM VITAE NORMAN J. WICKETT Assistant Conservation Scientist Genomics & Bioinformatics Chicago Botanic Garden 1000 Lake Cook Road Glencoe, IL 60022 Phone: 847.835.8280 Fax: 847.835.5484 Email: nwickett@chicagobotanic.org
NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees
NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees Erin Molloy and Tandy Warnow {emolloy2, warnow}@illinois.edu University of Illinois at Urbana
UoN, CAS, DBSC BIOL102 lecture notes by: Dr. Mustafa A. Mansi. The Phylogenetic Systematics (Phylogeny and Systematics)
- Phylogeny? - Systematics? The Phylogenetic Systematics (Phylogeny and Systematics) - Phylogenetic systematics? Connection between phylogeny and classification. - Phylogenetic systematics informs the
Gametophyte. (n) (2n) Sporangium. Sporophyte. (2n) N N
Tetrads of spores (n) Spores (n) Gametophyte (n) Archegonium with egg (n) Antheridium with sperm (n) fertilization Meiosis Zygote (2n) Spore mother cell (2n) Sporangium (2n) Sporophyte (2n) Embryo (2n)
Plant Diversity & Evolution (Outline)
Plant Diversity & Evolution (Outline) Review the Life cycle of Fungi Characteristics of organisms in the Kingdom Plantae. Evolution of plants: Challenges and adaptations to living on land Highlights of
Domain Eukarya: Kingdom Plantae non-vascular plants
Domain Eukarya: Kingdom Plantae non-vascular plants Land plants descended from a green algae ancestor Some key characteristics of land plants are shared with green algae, like Multicellular, eukaryotic,
Phylogenetics - Orthology, phylogenetic experimental design and phylogeny reconstruction. Lesser Tenrec (Echinops telfairi)
Phylogenetics - Orthology, phylogenetic experimental design and phylogeny reconstruction Lesser Tenrec (Echinops telfairi) Goals: 1. Use phylogenetic experimental design theory to select optimal taxa to
C3020 Molecular Evolution. Exercises #3: Phylogenetics
C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from
Bio 1B Lecture Outline (please print and bring along) Fall, 2007
Bio 1B Lecture Outline (please print and bring along) Fall, 2007 B.D. Mishler, Dept. of Integrative Biology 2-6810, bmishler@berkeley.edu Evolution lecture #5 -- Molecular genetics and molecular evolution
Construc)ng the Tree of Life: Divide-and-Conquer! Tandy Warnow University of Illinois at Urbana-Champaign
Construc)ng the Tree of Life: Divide-and-Conquer! Tandy Warnow University of Illinois at Urbana-Champaign Phylogeny (evolutionary tree) Orangutan Gorilla Chimpanzee Human From the Tree of the Life Website,
What is a Plant? Plant Life Cycle. What did they evolve from? Original Habitat 1/15/2018. Plant Life Cycle Alternation of Generations
What is a Plant? Multicellular Eukaryotic Autotrophic (photosynthesis) Has cell walls containing cellulose Lack mobility (sessile) Display Alternation of Generations in their life cycle Introduction to
Announcements. Lab Quiz #1 on Monday: (30pts) conifers + cones, vegetative morphology. Study: Display case outside HCK 132 with labeled conifers
Announcements Lab Quiz #1 on Monday: (30pts) conifers + cones, vegetative morphology Study: Display case outside HCK 132 with labeled conifers Movie: Sexual Encounters of the Floral Kind Intro to Keying/Greenhouse
A phylogenomic toolbox for assembling the tree of life
A phylogenomic toolbox for assembling the tree of life or, The Phylota Project (http://www.phylota.org) UC Davis Mike Sanderson Amy Driskell U Pennsylvania Junhyong Kim Iowa State Oliver Eulenstein David
Topic 2: Plants Ch. 16,28
Topic 2: Plants Ch. 16,28 Characteristics of Plants p. 316 1. Multicellular eukaryotic organisms 2. Composed of tissues, organs and organ systems. 3. Cell walls made of cellulose. 4. Store energy as starch.
Unit 7: Plant Evolution, Structure and Function
Time: 7 Days (some time spent working over breaks on this topic) and then an exam 16% of the AP Exam is on this material. Topics Covered: Reproduction, growth, and development Structural, physiological,
Chapter 1-Plants in Our World
Chapter 1-Plants in Our World Formation of earth-4.5-4.6 billion years ago Evidence of life from organic material-3.8 billion years ago Many cyanobacteria are photosynthetic, but these microscopic organisms
ASTRAL: Fast coalescent-based computation of the species tree topology, branch lengths, and local branch support
ASTRAL: Fast coalescent-based computation of the species tree topology, branch lengths, and local branch support Siavash Mirarab University of California, San Diego Joint work with Tandy Warnow Erfan Sayyari
Chapters 29 & 30: Plant Diversity
Chapters 29 & 30: Plant Diversity AP Biology 2013 1 Chara species, a pond organism 5 mm Colonization of the Land Coleochaete orbicularis, a disk-shaped charophyte that also lives in ponds (LM) Since colonizing
A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution Across the Poales
Kennesaw State University DigitalCommons@Kennesaw State University Faculty Publications 3-7-2016 A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution Across the Poales Michael R. McKain
From algae to angiosperms inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
Ruhfel et al. BMC Evolutionary Biology 2014, 14:23 RESEARCH ARTICLE Open Access From algae to angiosperms inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes Brad R Ruhfel
PHYLOGENOMIC PLACEMENT OF ANCIENT POLYPLOIDY EVENTS WITHIN THE POALES AND AGAVOIDEAE (ASPARAGALES) MICHAEL RAMON MCKAIN
PHYLOGENOMIC PLACEMENT OF ANCIENT POLYPLOIDY EVENTS WITHIN THE POALES AND AGAVOIDEAE (ASPARAGALES) by MICHAEL RAMON MCKAIN (Under the Direction of James H. Leebens-Mack) ABSTRACT Polyploidy has been an
Processes of Evolution
15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection
Plants Have Changed the World
Chapter 19 Plants Man: G. R. "Dick" Roberts/Natural Sciences Image Library Copyright McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill
Kingdom Plantae. Biology : A Brief Survey of Plants. Jun 22 7:09 PM
Kingdom Plantae Biology 2201 6.1 6.2 : A Brief Survey of Plants The study of plants is called botany. Plants are believed to have evolved from green algae. The main plant (land) characteristics are as
Adaptive Radiations. Future of Molecular Systematics. Phylogenetic Ecology. Phylogenetic Ecology. ... Systematics meets Ecology...
Future of Molecular Systematics... Systematics meets Ecology... 1. Biogeography 2. Ecology 3. Genomics Ecology and phylogenetics intertwined in a number of new fields of study called Phylogenetic Ecology:
Biology 11 Kingdom Plantae: Algae and Bryophyta
Biology 11 Kingdom Plantae: Algae and Bryophyta Objectives By the end of the lesson you should be able to: State the 3 types of algae Why we believe land plants developed from algae Lifecycle of a bryophyte
Evolution of Body Size in Bears. How to Build and Use a Phylogeny
Evolution of Body Size in Bears How to Build and Use a Phylogeny Lesson II Using a Phylogeny Objectives for Lesson II: 1. Overview of concepts 1. Simple ancestral state reconstruction on the bear phylogeny
Chapter What is a Plant? Biology. Slide 1 of 33. End Show. Copyright Pearson Prentice Hall
Chapter 22.1 Biology What is a Plant? 1 of 33 Objectives 1. Describe the basic characteristics of life. 2. Describe what plants need to survive. 3. Describe the life cycle of plants. 4. Describe how the
Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?
Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species
9. The rhizoids of seedless nonvascular plants are comparable to the of a seed plant.
Name: # Date: Science Chapter 5 Study Guide 1. List three adaptations that allow plants to survive on land? 2. List three characteristic of plants. 3. Why is binomial nomenclature used to name plants?
Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny -- concordance with developmental evidence
Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny -- concordance with developmental evidence Xiaohan Yang*, Gerald A. Tuskan*, Timothy J. Tschaplinski, (Max) Zong-Ming Cheng* *Department
Classification of Plants
Classification of Plants Plants Aquatic Plants Ex. green algae Similarities between green algae and land plants: A) have chlorophylls a and b B) cellulose cell walls C) store food energy in the form of
STUDY QUESTIONS TEST 2 ANTHOCEROPHYTA, TRACHEOPHYTES AND PLANT STRUCTURE
STUDY QUESTIONS TEST 2 ANTHOCEROPHYTA, TRACHEOPHYTES AND PLANT STRUCTURE 1. Name the Bryophyte phylum that is most closely related to vascular plants? 2. How do Anthocerophyta differ from other Bryophytes?
Plant Diversity I: How Plants Colonized Land
LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 29 Plant Diversity I: How Plants
Upcoming challenges in phylogenomics. Siavash Mirarab University of California, San Diego
Upcoming challenges in phylogenomics Siavash Mirarab University of California, San Diego Gene tree discordance The species tree gene1000 Causes of gene tree discordance include: Incomplete Lineage Sorting
Comparative Genomics II
Comparative Genomics II Advances in Bioinformatics and Genomics GEN 240B Jason Stajich May 19 Comparative Genomics II Slide 1/31 Outline Introduction Gene Families Pairwise Methods Phylogenetic Methods
Stage 1: Karyotype Stage 2: Gene content & order Step 3
Supplementary Figure Method used for ancestral genome reconstruction. MRCA (Most Recent Common Ancestor), AMK (Ancestral Monocot Karyotype), AEK (Ancestral Eudicot Karyotype), AGK (Ancestral Grass Karyotype)
Plants. and their classi.ication
+ Plants and their classi.ication +Why are plants important? n Photosynthesis Carbon dioxide + water + energy à sugar + oxygen 6CO 2 + 6H 2 O à C 6 H 12 O 6 + 6O 2 n Food (green tea, fruits, seeds, roots,
BIOINFORMATICS LAB AP BIOLOGY
BIOINFORMATICS LAB AP BIOLOGY Bioinformatics is the science of collecting and analyzing complex biological data. Bioinformatics combines computer science, statistics and biology to allow scientists to
PSI Biology Classification Classification
Classification Classification & Naming Classwork 1. What is the correct order of the current classification hierarchy, from most general to most specific? 2. Are two organisms in domain more or less closely
Kingdom Plantae. A Brief Survey of Plants
Kingdom Plantae A Brief Survey of Plants The study of plants is called botany. Plants are believed to have evolved from green algae. The main plant (land) characteristics are as follows: 1. Common cellular
Computational methods for predicting protein-protein interactions
Computational methods for predicting protein-protein interactions Tomi Peltola T-61.6070 Special course in bioinformatics I 3.4.2008 Outline Biological background Protein-protein interactions Computational
Exam 1 Review: Supplemental Instruction Iowa State University
Exam 1 Review: Supplemental Instruction Iowa State University Leader: Elizabeth Course: Bio 211 Instructor: Dr. Deitloff Date: 2/6/2014 1. Which is not a characteristic of a hypothesis? a. It is falsifiable.
Prokaryote vs. Eukaryote
DIVERSITY OF LIVING THINGS Prokaryote vs. Eukaryote 1. Test Monday 2. Lab Report Rough Draft (typed) due Wednesday 3. Lab Report Due Friday Oct 7th 4. Letter to MP due Tuesday Oct 11 th CAROLUS LINNAEUS
SPECIATION. REPRODUCTIVE BARRIERS PREZYGOTIC: Barriers that prevent fertilization. Habitat isolation Populations can t get together
SPECIATION Origin of new species=speciation -Process by which one species splits into two or more species, accounts for both the unity and diversity of life SPECIES BIOLOGICAL CONCEPT Population or groups
4/30/2014. The lives of modern plants and fungi are intertwined We depend on plants and indirectly, fungi for much of our food.
and the Colonization of Land The lives of modern plants and fungi are intertwined We depend on plants and indirectly, fungi for much of our food. Plants are often harmed by fungi. On the other hand, nearly
Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega
BLAST Multiple Sequence Alignments: Clustal Omega What does basic BLAST do (e.g. what is input sequence and how does BLAST look for matches?) Susan Parrish McDaniel College Multiple Sequence Alignments
Chapter 13- Reproduction, Meiosis, and Life Cycles. Many plants and other organisms depend on sexual reproduction.
Chapter 13- Reproduction, Meiosis, and Life Cycles Many plants and other organisms depend on sexual reproduction. Flowers are the sexual reproductive organ systems of angiosperms. Sexual reproduction gametes
Evidence for Evolution
Evidence for Evolution Evidence for Evolution - Common Ancestry Classification Hierarchical distribution of traits trees Homology Vestigial Structures Fossil record Biogeography use tree metaphor Variation
Evidence for Evolution. Evidence for Evolution - Common Ancestry. Darwin s Tree Thinking. Classification Hierarchical distribution of traits
Evidence for Evolution Evidence for Evolution - Common Ancestry Classification Hierarchical distribution of traits trees Homology Vestigial Structures Fossil record Biogeography use tree metaphor Variation
Plant Diversity I: How Plants Colonized Land
Chapter 29 Plant Diversity I: How Plants Colonized Land PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions
Session 5: Phylogenomics
Session 5: Phylogenomics B.- Phylogeny based orthology assignment REMINDER: Gene tree reconstruction is divided in three steps: homology search, multiple sequence alignment and model selection plus tree
Basal angiosperms, and plant breeding systems. Angiosperm phylogeny
Basal angiosperms, and plant breeding systems Angiosperm phylogeny Soltis et al., 2011 Ranunculaceae' Monocots' Magnoliids' ANITA'grade' Basal angiosperms Angiosperm phylogeny A N A ANITA grade Amborella
Anatomy of a species tree
Anatomy of a species tree T 1 Size of current and ancestral Populations (N) N Confidence in branches of species tree t/2n = 1 coalescent unit T 2 Branch lengths and divergence times of species & populations
BIOLOGY 317 Spring First Hourly Exam 4/20/12
Name: Lab sect. (TA name/time): BIOLOGY 317 Spring 2012 First Hourly Exam 4/20/12 1) (24 pts) Match the letter of the family given on the right with the characteristics for a plant described on the left.
Biology 2201 Unit Test Holy Spirit High Mr. Pretty Name: ANSWER KEY
Biology 2201 Unit Test Holy Spirit High Mr. Pretty Name: ANSWER KEY 1.) Which of the following increases as you proceed down classification levels from kingdom to species? A) Activity B) Diversity among
Phylogenetic inference
Phylogenetic inference Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, March 7 th 016 After this lecture, you can discuss (dis-) advantages of different information types
Organizing Life s Diversity
17 Organizing Life s Diversity section 2 Modern Classification Classification systems have changed over time as information has increased. What You ll Learn species concepts methods to reveal phylogeny
Example of Function Prediction
Find similar genes Example of Function Prediction Suggesting functions of newly identified genes It was known that mutations of NF1 are associated with inherited disease neurofibromatosis 1; but little
Plants and Fungi. Bryophytes Bryophytes, most commonly mosses Sprawl as low mats over acres of land
Plants and Fungi Terrestrial Adaptations of Plants Structural Adaptations A plant is a multicellular eukaryote and a photoautotroph, making organic molecules by photosynthesis In terrestrial habitats,
Sequenced Mitochondrial Genomes of Bryophytes
Mitochondrial Genomes of Bryophytes 1 Sequenced Mitochondrial Genomes of Bryophytes Asheesh Shanker Department of Bioscience and Biotechnology, Banasthali University, Rajasthan, India Abstract: The determination
Unit 2B- The Plants. Plants can be classified according to the presence or absence of vascular tissue.
Unit 2B- The Plants Botany is the study of plants. All plants are said to have a common ancestor; (ie.) it is thought that plants have evolved from an ancient group of green algae. Plants and green algae
Comparative genomics: Overview & Tools + MUMmer algorithm
Comparative genomics: Overview & Tools + MUMmer algorithm Urmila Kulkarni-Kale Bioinformatics Centre University of Pune, Pune 411 007. urmila@bioinfo.ernet.in Genome sequence: Fact file 1995: The first
Bi 151 Plant Morpho-anatomy Lecture 1. What are plants??? Kingdom Plantae (plants) 6/26/2014. What are some structural features of plants?
Bi 151 Plant Morpho-anatomy Lecture 1 What are plants??? Plants: General Structural Features Jan Lorie M. Robil, M.Sc. Kingdom Plantae (plants) 1. Multicellular 2. Autotrophs (chloroplasts) 3. Cellulose
The Producers: The Plant Kingdom An Introduction to Plants and the Mosses
The Producers: The Plant Kingdom An Introduction to Plants and the Mosses Mosses Phylum Bryophyta - ~12,000 species Liverworts - Phylum Hepaticophyta - ~8,500 species Hornworts - Phylum Anthocerophyta
The move from water to land. The move from water to land. Chapter 16- Evolution of Plants. Green algae are the ancestors to all plants
Chapter 16- Evolution of Plants From Protists to Plants Moving right along! Green algae are the ancestors to all plants Who, ME? Wow I feel so important! Charophyceans 475 million years ago, shallow seas
Plant Vocabulary. Define
Define Plant Vocabulary 1. Photosynthesis 2. Eukaryotic 3. Monocot 4. Dicot 5. Cotyledon 6. Roots 7. Stems 8. Leaves 9. Xylem 10. Phloem 11. Capillary action 12. Meristem 13. Apical meristem 14. Vascular
Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST
Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Introduction Bioinformatics is a powerful tool which can be used to determine evolutionary relationships and
Test Lesson 18 Plants - Answer Key Page 1
Test Lesson 18 Plants - Answer Key Page 1 1. Algae are. A. protists B. early plants C. multicellular eukaryotes D. forms of euglenia 2. Algae reproduce by what two methods? A. conjugation and meiosis B.
Test Lesson 18 Plants Page 1
Test Lesson 18 Plants Page 1 1. Algae are. A. protists B. early plants C. multicellular eukaryotes D. forms of euglenia 2. Algae reproduce by what two methods? A. conjugation and meiosis B. binary fission