Plant molecular systematics
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Plant Molecular Systematics. Spring 2013. “Problems” with morphological data…. Convergence and parallelisms Reduction and character loss Phenotypic vs. genotypic differences Evaluation of homology Misinterpretation of change or polarity Limitation on number of characters

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Plant Molecular Systematics

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Plant molecular systematics

Plant Molecular Systematics

Spring 2013


Problems with morphological data

“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


Always searching for new types of characters

Always searching for new types of characters…

Is molecular data intrinsically better than morphological data?


Plant molecular systematics

Central Dogma


Plant molecular systematics

Central Dogma

Lipid pigments:

chlorophyll

lycopenes

xanthophylls

carotene

Iridoid

compounds

Terpenes

Alkaloids

(N-containing)

e.g. nicotine

caffeine

morphine

betalains

Phenolics:

flavonols

flavones

tannins

anthocyanins

Secondary Metabolites


Development of molecular chemical systematic methods chemosystematics

Development of Molecular (Chemical) Systematic Methods“Chemosystematics”

  • 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 – 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 direct estimates of genetic relationships based on allele frequency of enzyme variants


Molecular dna systematics

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 increasingly even whole genomes relatively quickly


Molecular systematics

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


Plant molecular systematics

How big are genomes of organisms?


Plant molecular systematics

Genomes of the Plant Cell

Plastid

Nuclear

Mitochondrial


Three genomes in plant cells

Three genomes in plant cells

Mitochondrion

200,000-

2,500,000 bp

Generally

maternally

inherited

(seed parent)

Chloroplast

135,000-

160,000 bp

Generally

maternally

inherited

(seed parent)

Nucleus

1.1 x 106

to 1.1 x 1011

kilobase pairs

Biparentally

inherited


Selection of dna region to compare

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


Genes frequently used for phylogenetic studies of plants

Genes frequently used for phylogenetic studies of plants:

  • Mitochondrial genome – uniparentally (maternally) inherited, but genes evolve very slowly and structural rearrangements happen very frequently, so generally not useful in studying relationships, but there are some exceptions

  • Plastid genome – uniparentally (maternally) 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

    - many other genes now with next generation sequencing


Plant molecular systematics

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

  • photosynthesis and

  • protein synthesis

Fig. 14.4


Plant molecular systematics

The Polymerase Chain Reaction (PCR) (Fig. 14.2)


Plant molecular systematics

Automated Sequencing

Scanning of gel to detect

fluorescently-labeled

DNAs; data fed directly to

computer.


Plant molecular systematics

Fig. 14.3


How do we analyze molecular variation

How do we analyze molecular variation?

- DNA nucleotide sequences (point mutations)- Structural rearrangements-insertions and deletions (indels)-inversions


Plant molecular systematics

Aligned DNA sequences showing substitutions


Plant molecular systematics

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)


Plant molecular systematics

A molecular synapomorphy for Subfamily Cactoideae

(Cactaceae) – deletion of the plastid rpoC1 intron…

ancestral

derived

(Wallace & Cota, Current Genetics, 1995)


Cactaceae trnl intron deletions

Cactaceae: trnL Intron Deletions


Plant molecular systematics

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)


Plant molecular systematics

Chloroplast DNA Inversion

23 kb inversion in all Asteraceae except for members of

Tribe Barnadesieae (now Subfamily Barnadesioideae)


Plant molecular systematics

Fig. 14.6


Comparative dna sequencing

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


Plant molecular systematics

Partial sequence of rbcL (plastid gene coding for

Rubisco) in Poaceae


Plant molecular systematics

Anomochlooideae

Pharoideae

Puelioideae

BEP Clade

Bambusoideae

(bamboos)

Pooideae

(bluegrasses, wheat)

Ehrhartoideae

(rices and allies)

Aristidoideae

(wiregrasses)

Stamens

reduced to 3;

+ 55 mya

Panicoideae

(maize, panicgrasses)

Chloridoideae

(love grasses)

PACMAD Clade

Danthonioideae

(pampas grasses)

Micrairoideae

Arundinoideae

(reeds)

Crepet & Feldman 1991


Plant molecular systematics

Data mining

Climatic Data

-Global Biodiversity

Information Facility (GBIF)

-1,584,351 independent

collection sites

-10,469 taxa

Edwards et al., Science 2010, Fig. 4

Genetic Data

-2,684 taxa

-8 regions (plastid

and nuclear)

-phylogenetic analysis

Edwards & Smith, PNAS 2010, Fig. 1


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