Plant Speciation

1
Plant Speciation Evolution (PBIO 475/575)

• Molecular Components
• of Heredity

2
DNA Double Helix

• Sugar-phosphate backbone
• Base-pair "rungs" of ladder
• Nucleotides attached to S-P molecules
• Strands antiparallel (run in opposite directions,
  5'--3')

Raven et al. (1992)
3
DNA Double Helix

• Each base-pair "rung" has a purine (A or G) and
  pyrimidine (C or T)
• Strands held together by hydrogen bonds between
  nucleotides
• Chemical structures of nucleotides discourage
  "incorrect" pairing
• G-C pair has 3 hydrogen bonds, A-T only
  2--former is stronger

4
DNA Replication

• Semiconservative--replication results in two
  strands, one original and one new
• Sequence of events
• Helix unwinds
• Both strands replicate simultaneously, during
  unwinding process

Raven et al. (1992)
5
DNA Replication

• Sequence of events (cont.)
• "Leading" strand replicates continuously from 3'
  end
• newest end of forming strand oriented toward
  replication fork
• "Lagging" strand replicates by a series of
  fragments placed end-to-end, facing away from
  fork fragments with newest ends of fragments
  later "ligated"
• 2 polymerases "proofread" for mismatched bases

6
Physical Structure of Genes

• Segments of chromatin that yield proteins through
  transcription, translation
• Typically separated by stretches of inactive
  chromatin (intergenic spacers)
• Commonly encompasses short stretches of inactive
  chromatin that get cut out during translation
  (introns)
• Can experience recombination in whole or in part!
  (contrary to original theories)

7
Physical Structure of Genes

• Fundamental components
• Promoter region "upstream" of initiation site
• Necessary binding site for RNA polymerase to
  accomplish translation
• Bears recognition sequences for enzyme (e.g.,
  TTTA)
• Initiation site for transcription--yields
  ribosomal binding site in mRNA

Suzuki et al. (1989)
8
Gene Structure and Function

• Fundamental components (cont.)
• Coding region (exon) of structural gene
• Composed of codons (triplets) of nucleotides
• Begins with start codon (e.g., TAA)
• Ends with stop codon
• Codons complementary to mRNA codons
• -- amino acids in ultimate protein chain
• Termination region--halts polymerase from
  transcribing

9
Transcription

• Transcription from DNA strand in nucleus
• Takes place in three areas of DNA strand
• One site codes for large small subunits of rRNA
• Second site downstream codes for tRNAs
• Third site further downstream codes for proteins
• Nucleotides assembled parallel to DNA
• Complementary nucleotides used AU, CG

Suzuki et al. (1989)
10
Post-transcriptional Processes

• Processing of primary RNA transcript from
  protein-coding DNA
• 5' cap and 3' poly-A tail stuck on
• introns spliced out in several stages, bringing
  exons into proximity
• Processing in different organs eliminates
  different portions of transcript
• -- different mRNA products from initial
  transcript

Suzuki et al. (1989)
11
Post-transcriptional Processes

• rRNA and tRNAs move into cytoplasm through
  nuclear pores immediately
• Mature mRNA moves into cytoplasm after processing
  completed
• Genes of mature mRNA translated to proteins
• Ribosomal subunits attach to mRNA (usually
  several at different points)
• tRNAs bring amino acids corresponding to mRNA
  codons into proximity of ribosomal complex
• Amino acids joined by peptide bonds to form
  protein chain
• No "proofreading" functions by RNA polymerases

12
Post-transcriptional Processes

• MicroRNAs (miRNAs)newly discovered, very small
  RNAs that bind to trancripts and render them
  non-functional (Griffiths et al. 2008)
• play potentially huge role in accomplishing
  heterochronic (time-shifting) or tissue-specific
  gene expression
• Hundreds of loci found in typical genomes, appear
  to be produced from junk DNA regions
• miRNA abundance and diversity influenced by
  environmental conditions
• Heritable in the next generationhence
  Lamarckian in behavior!

13
The Genetic Code

• Degeneracy of the code
• 4 nucleotides, organized into triplets, yield 64
  possible combinations
• 20 commonly employed amino acids
• Multiple "synonymous" codons for many amino acids

Raven et al. (1992)
14
The Genetic Code

• Codon-anticodon pairing
• Third position "wobble"--sloppy pairing for last
  nucleotide in codon
• mRNA codons with G or U in third position will
  recognize and accept more than one tRNA anticodon

15
Regulatory Genes

• Determine or influence timing, placement or
  extent of structural gene (enzyme-producing gene)
  action
• Regulation most common at the transcriptional
  level
• Effects most far-reaching (especially
  morphologically) of all possible regulatory types
• Results from "switching" on and off of gene
  transcription for particular genes
• Simple systemencompasses some but not all
  genetic systems

16
Regulatory Genes

• "Multiple" systemsmay represent multiple genes,
  promoters, regulators or combos of these
• Originate from duplications, can diverge later

Langridge (1991)
17
Enzyme Architecture
Computer-simulated folding of rubisco

• Primary--linear sequence of amino acids
• Secondary--side-group interactions
• alpha-helix
• beta-pleated sheet

Kellogg Juliano (1997)
18
Enzyme Architecture

• Tertiary--folding of secondary components
• Quaternary--multimeric associations among
  tertiary elements
• Protein structure at any or all levels can impact
  or determine enzymatic function

19
Enzymatic Pathways

• One gene-one enzyme hypothesis
• One gene controls production of a single enzyme
• A biochemical reaction is catalyzed by one enzyme
• Processes occur as a series of catalyzed
  reactions each ultimately regulated by a
  different gene

Suzuki et al. (1989)
20
Enzymatic Pathways

• Metabolic cycles
• e.g., photosynthesis
• e.g., flavonoids
• Usually slow to evolve
• Would have been important early on in evolution
  of land plants
• Increased complexity, integration--now largely
  regulatory adjustments, at least among closely
  related species

21
Enzymatic Pathways

• Development/morphology
• e.g., pollination mechanisms in orchids
• May evolve very rapidly
• Slight changes by many different genes yield
  major cumulative changes--new adaptive complexes
  in a radiating lineage
• Slight individual (developmental) modifications
  to morphology accompanied by biochemical
  adjustments

22
Regulatory vs. Structural Genetic Change

• Example 1--Studies of duplicate gene expression
  in catastomid fishes
• Family originated from polyploidy ca. 50 million
  years ago
• 15 species now extant
• Half of duplicated genes in polyploids have lost
  expression

23
Regulatory vs. Structural Genetic Change

• Example 1--Studies of duplicate gene expression
  in catastomid fishes (cont.)
• Remainder have altered in expression in 60 of
  tissues studied
• Most changes in duplicate gene expression relate
  to different organ and tissue locations, not to
  cell type or developmental stage
• Only 12/84 divergent tissue expressions traceable
  to enzyme-coding gene mutations
• Most tissue-characteristic enzyme patterns have
  therefore resulted from mutations in
  transcriptional or processing stages of
  RNA?regulatory elements

24
Regulatory vs. Structural Genetic Change

• Example 2--Surveys of tryptophan biosynthetic
  pathways in protists and fungi
• Regulation mechanisms are at least as easily
  modified as gene locations (chromosome
  structural changes)
• Much more readily altered than primary structure
  of active enzymes?more evidence of rapid changes
  in regulatory mechanism

25
Regulatory vs. Structural Genetic Change

• Example 3--Hybrids between morphologically very
  similar taxa of fish
• Express ontogenetic disturbances, e.g., increases
  in morphological abnormalities, lethality
• Species very closely related, probably only
  recently diverged (not sufficient time for
  extensive genetic differentiation of structural
  genes
• Species divergence must be in the molecular
  regulation of genes underlying morphological
  traits

26
Organization of Genetic Material

• Hierarchical arrangement
• DNA strands paired in a double helix
• Chromatin "beads on a string"--double helix wound
  helically around 8-part histone molecule, as
  chain of "nucleosomes"
• Nucleosomes packed into a tight "solenoid"
  ("supercoiling")
• Packed stretches of nucleosomes for part of
  condensed chromosomes

Raven et al. (1992)
27
Organization of Genetic Material

• Multiple-copy DNA
• Dispersed repetitive DNA
• Scattered throughout genome
• Minisatellites--complicated motifs,
  dozens/hundreds of bp long
• Microsatellites--simple repeat motifs, usually
  
• Considered "junk" DNAbut may accidentally become
  involved in transcription through accidents of
  replication
• Gene families
• Copies in different locations, i.e., on different
  chromosomes
• e.g., ribosomal genes, histone genes
• concerted evolution in some families
  homogenizes sequence across all locibut is
  random in direction, can proceed with different
  templates across populations

28
Mendelian Principles

• Alleles--different phenotypic expressions of the
  same genetic trait
• Dominance relationships
• Complete dominance
• Dominant allele--expresses phenotype if only one
  copy is present
• Recessive allele--only expresses phenotype if
  both copies are present

Raven et al. (1992)
29
Mendelian Principles

• Other dominance relationships
• Incomplete dominance--intermediate phenotype in
  heterozygote
• Codominance--both phenotypes expressed in
  heterozygote (e.g., blood types LmLm, LnLn and
  LmLn)

30
Mendelian Principles

• Allelic systems
• Classical 2-alleletraditional model
• Multiple allelic series
• Documented for many genes, often with non-simple
  relationships
• e.g., chevron leaf pattern of white clover
• e.g., incompatibility systems enforcing
  outcrossing

31
Mendelian Principles

• Genotypes
• Homozygote--both alleles are the same
• Homozygous dominant (AA)expresses phenotype
  coded by the dominant allele
• Homozygous recessive (aa)expresses phenotype
  coded by the recessive allele
• Heterozygote--alleles are different (Aa)
  expresses phenotype of dominant allele if
  dominance relationship is dominant type, but
  something intermediate or divergent where
  relationship is incomplete or codominant

32
Mendelian Principles

• Mendel's laws
• Law of Segregation
• Members of a gene pair segregate into separate
  gametes
• One-half of the gametes has one member, the other
  half, the other
• Law of Independent assortment--during gamete
  formation, segregation in each gene pair is
  independent of other pairs

Suzuki et al. (1989) Raven et al. (1992)
33
Other Genetic Effects

• Lethal genes
• Death in recessive homozygote harboring lethal
  alleles
• Sometimes skews progeny ratios where
  heterozygotes are "subvital"
• Pleiotropy--one allele affects two or more
  characters, e.g., coat color and survival in
  yellow mice
• Epistasis--phenotypic expression of one gene
  dependent on expression of another gene
• Suppressor genes
• Modifier genes
• Duplicate genes
• NOTEmany of these are non-Mendelian or even
  non-Darwinian in inheritance!

34
Mitotic and Meiotic Products

• Mitosis
• Occurs in somatic cells
• Yields two daughter cells from one
• Daughters diploid, same as parent
• Daughters typically genotypically identical to
  each other and to parent
• Usually disregarded in terms of heritable
  variation (but consider somatic mutations
  affecting flower primordia)

Mitosis
Meiosis
Raven et al. (1992)
35
Mitotic and Meiotic Products

• Meiosis
• Occurs in generative cells ("sex cells")
• Yields, ultimately, four daughter cells from one
• Daughters haploid, reduced from diploid parent
  (meiocyte)
• Daughters typically genotypically different from
  each other and from parent
• Primary point where mutations are incorporated as
  heritable variation

36
Crossing-over

• Commonly accompanies meiosis, at the
  "four-strand" stage
• Occurs usually between any two nonsister
  chromatids
• Begins with intertwining of homologous
  chromosomes ("chiasmata")

Suzuki et al. (1989)
37
Crossing-over

• Intertwined strands break at chiasmata and
  reunite, with exchange of chromosome parts
• Typically crossing-over is equal--same-sized
  fragments broken at same point and swapped,
  yielding structurally identical chromatids
• 50 or fewer progeny are recombinant
• Generates huge numbers of new recombinant
  genotypes, at each sexual reproductive cycle, in
  each individual, in each population, across the
  species!

38
Crossing-over

• Multiple crossing-over events
• Double crossing-over between adjacent sister
  chromatids yields double recombinants
• Crossing-over also takes place among non-adjacent
  chromatids
• Interference
• In some areas of chromosomes double crossing-over
  never occurs
• Suggests non-independence of crossing-over in
  some regions

39
Bibliography

• Griffiths, A. J. F., S. R. Wessler, R. C.
  Lewontin, and S. B. Carroll. 2008. Introduction
  to genetic analysis, 9th ed. W. H. Freeman and
  Company, New York, New York. 838 pp.
• Kellogg, E. A. and N. D. Juliano. 1997. The
  structure and function of RuBisCO and their
  implications for systematic studies. American
  Journal of Botany 84413-428.
• Langridge, J. 1991. Molecular genetics and
  comparative evolution. John Wiley Sons, Inc.,
  New York, New York. 216 pp.

40
Bibliography

• Raven, P. H., R. F. Evert, and S. E. Eichhorn.
  1992. Biology of plants, 5th ed. Worth
  Publishers, New York, New York. 791 pp.
• Suzuki, D. T., A. J. F. Griffiths, J. H. Miller,
  and R. C. Lewontin. 1989. An introduction to
  genetic analysis, 4th ed. W. H. Freeman and
  Company, New York, New York. 768 pp.