Plant Molecular Systematics - PowerPoint PPT Presentation

View by Category
About This Presentation
Title:

Plant Molecular Systematics

Description:

Plant Molecular Systematics Spring 2011 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Problems with morphological data Convergence and ... – PowerPoint PPT presentation

Number of Views:1056
Avg rating:3.0/5.0
Date added: 18 May 2020
Slides: 32
Provided by: eeobIasta
Category:

less

Write a Comment
User Comments (0)
Transcript and Presenter's Notes

Title: Plant Molecular Systematics


1
Plant Molecular Systematics
Spring 2011
2
Problems with morphologicaldata
  • Convergence and parallelisms
  • Reduction and character loss
  • Phenotypic vs. genotypic differences
  • Evaluation of homology
  • Misinterpretation of change or polarity
  • Limitation on number of characters
  • Phenotypic plasticity

3
Always searching for new types of characters
Is molecular data intrinsically better than
morphological data?
4
Central Dogma
Lipid pigments chlorophyll lycopenes
xanthophylls carotene
Phenolics flavonols flavones tannins
anthocyanins
Iridoid compounds
Alkaloids (N-containing) e.g. nicotine
caffeine morphine betalains
Terpenes
Secondary Metabolites
5
Development of Molecular (Chemical) Systematic
MethodsChemosystematics
  • Early methods relied on chromatography to
    separate complex mixtures of secondary
    metabolites, detect them, and then compare
    between taxa spot botanists very phenetic
  • Better separation and identification methods
    developed (HPLC, MS) used pathway stages as
    cladistic characters - phytochemistry
  • Move away from secondary metabolites to proteins
  • Early protein studies used immunological
    reactions
  • Development of improved electrophoretic methods
    permitted direct protein comparisons between taxa
  • Comparison of seed storage proteins
  • Development of allozyme techniques direct
    estimates of genetic relationships based on
    allele frequency

6
Molecular (DNA) Systematics
  • Next step was to examine DNA directly through
    examination and comparison of restriction
    fragments (RFLP bands)
  • Technology evolved to make it feasible to
    sequence DNA directly
  • Initially limited to single genes or non-coding
    regions
  • Now feasible to sequence large numbers of genes
    or regions or even whole genomes relatively
    quickly

7
Molecular Systematics
  • Can obtain phylogenetically informative
    characters from any genome of the organism-
    Assumes that genomes accumulate molecular changes
    by lineage, as morphological characters do-
    Possibly greater assurance of homology with
    molecular data (less likely to misinterpret
    characters) but homoplasy happens!- Principal
    advantages are the much greater number of
    molecular characters available greater
    comparability across lineages

8
Genomes of the Plant Cell
Plastid
Nuclear
Mitochondrial
9
Table 5.1 from the text
10
Selection of DNA region to compare
  • Should be present in all taxa to be compared
  • Must have some knowledge of the gene or other
    genomic region to develop primers, etc.
  • Evolutionary rate of sequence changes must be
    appropriate to the taxonomic level(s) being
    investigated slow genes versus fast genes
  • It is desirable that sequences can be readily
    aligned
  • The biology of the gene (or other DNA sequence)
    must be understood to assure homology

11
Genes frequently used for phylogenetic studies of
plants
  • Mitochondrial genome uniparentally inherited,
    but genes evolve very slowly and structural
    rearrangements happen very frequently, so
    generally not useful in studying relationships
  • Plastid genome uniparentally inherited
  • - rbcL ribulose-bisphosphate carboxylase large
    subunit
  • - ndhF NADH dehydrogenase subunit F
  • - atpB ATP synthetase subunit B
  • - matK maturase subunit K
  • - rpl16 intron ribosomal protein L16 intron
  • Nuclear genome biparentally inherited
  • - ITS region internal transcribed spacers ITS1
    and ITS2
  • - 18S, 26S ribosomal nuclear DNA repeat
  • - adh alcohol dehydrogenase

12
Plastid Genome
  • Circular, derived
  • from endosymbio-
  • sis of cyanobacteria
  • Three zones
  • LSC (large single
  • copy region)
  • SSC (small single
  • copy region)
  • IR (inverted repeats)
  • - Genes related to
  • PS and protein
  • synthesis

Marchantia polymorpha - liverwort
13
Figure 5.1 from the text
14
The Polymerase Chain Reaction (PCR)
Figure 5.2 from the text
15
Automated Sequencing
Scanning of gel to detect fluorescently-labeled
DNAs data fed directly to computer.
16
(No Transcript)
17
(No Transcript)
18
(No Transcript)
19
How do we analyze molecular variation?
- DNA nucleotide sequences (point mutations)
- Structural rearrangements -insertions and
deletions (indels) -inversions
20
Partial sequence of rbcL (plastid gene coding for
Rubisco) in Poaceae
Figure 5.3 from the text
21
Insertion-Deletion Events
  • - Can occur as single
  • nucleotide gains or losses
  • or as lengths of 2-many
  • base pairs
  • Can also be chunks of
  • DNA (i.e., losses of introns)

22
A molecular synapomorphy for Subfamily Cactoideae
(Cactaceae) deletion of the plastid rpoC1
intron
(Wallace Cota, Current Genetics, 1995)
23
Cactaceae trnL Intron Deletions
24
trnL intron deletions Columnar Cacti
North American Clades
Pachycereeae
Leptocereeae
Hylocereeae
Corryocactus
Browningieae I
Browningieae II
- 268 bp
Cereeae
Shared Deletion 2
Trichocereeae
South American Clades
(Tribe Browningieae polyphyletic)
25
Chloroplast DNA Inversion
23 kb inversion in all Asteraceae except for
members of Tribe Barnadesieae (now Subfamily
Barnadesioideae)
26
(No Transcript)
27
Comparative DNA Sequencing
  • Obtain DNA samples from representative organisms
    (try to represent morphological diversity) and
    outgroups
  • Identify DNA region(s) for comparison
  • Use PCR to amplify targeted region
  • Carry out sequencing reactions
  • Run sequencing procedures (automated)
  • Align sequences
  • Use aligned sequences for phylogenetic analysis
    (various programs using various algorithms)
  • Evaluate data in context of taxonomy and
    morphology

28
Anomochlooideae
Pharoideae
Puelioideae
Bamboos (Bambusoideae)
Origin of grasses ca. 70-80 mya in forests
Bluegrasses (Pooideae)
Rices (Ehrhartoideae)
Panicgrasses (Panicoideae)
Major radiation in Oligocene- Miocene epochs into
open habitats
Needlegrasses (Aristidoideae)
Lovegrasses (Chloridoideae)

Micrairoideae
Stamens reduced to 3
Reeds (Arundinoideae)
Oatgrasses (Danthonioideae)
29
Phylogeny of Pooideae (multiple data sets)
Figure 5.5. from the text
30
Figure 5.7 from the text
31
Figure 5.4 from the text
About PowerShow.com