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BIO 3102
MOLECULAR EVOLUTION
• Study of evolution of macromolecules
- nature of changes (in DNA, protein) & their impact
Evolutionary change involves genetic change
D Genotype
D Phenotype
M.C. Escher “Sky & water”
• Use of molecular data to help reconstruct evolutionary history
- phylogenetic trees
modern species
extinct lineages
cenancestor - most recent
primordial life form
common ancestor
of extant organisms
Brown Fig.16.1
Closely-related organisms have more
similar protein sequences than
distant organisms
MOLECULAR CLOCKS
www.csmt.ewu.edu/.../ chem163/163LT1.html
“Web-of-life”
“Taking an axe to
the Tree of Life...”
Ford Doolittle
“... far more complex scenario than Darwin could have imagined...
Many [microbes] swap genes back and forth, or engage in gene duplication,
recombination, gene loss or gene transfers...”
www.whoi.edu/cms/images/oceanus/2005/4/v43n2-teske_edwards1en_8591.gif
Dalhousie University
News July 11, 2007
A
B
1. Which tree is more accurate?
2. Is the frog more closely related to the fish or to the human,
based on this tree?
“The tree-thinking challenge” Science 310:979, 2005
Extant
Fossil
Fossil
Schopf PNAS 91:6735, 1994
Volpe & Rosenbaum Fig.14.3
Mass extinctions, as well as radiations leading to taxonomic diversity
App1.Fig.2
“Loss and recovery of wings in stick insects”
Nature 421: 264, 2003
Male
Female
Winged
Partially
winged
Wingless
Morphological data
Phylogeny based on molecular data
EVOLUTIONARY INFORMATION FROM DNA SEQUENCES?
GENE
- sequence of DNA (or RNA) that is
essential for a specific function
1. Protein-coding genes
U.S. Dept of Energy Human Genome Program,
http://www.ornl.gov/hgmis
2. RNA-specifying genes
3. Functional DNA elements
- regulatory
- structural
Do not use term in text (p.9): “Untranscribed genes” for #3
“SILENT” GENE
- untranscribed, but potentially functional at DNA level
PSEUDOGENE
- non-functional DNA with high degree of similarity to a
functional gene
How can pseudogenes arise during evolution?
Orthologous genes
- descendants of an ancestral gene that was present
in the last common ancestor of two or more species
Paralogous genes
- arose by gene duplication within a lineage
“TYPICAL” EUKARYOTIC PROTEIN-CODING GENE
Where is the promoter? 5’ UTR ? 3’ UTR ?
What regions will be present in the mRNA?
Is there an error in this figure?
Fig.1.4
“TYPICAL” BACTERIAL GENE ORGANIZATION
How many promoters in this region?
How many proteins encoded?
Operon = cluster of co-transcribed genes
Evolutionary advantages of operon organization?
Fig.1.6
PROTEIN-CODING GENES
DNA
5’ …. ATG GGA TTG CCC GCC …. 3’
“coding strand”
3’ .… TAC CCT AAC GGG CGG …. 5’ “template strand”
mRNA 5’ …. AUG GGA UUG CCC GCC …. 3’
- DNA usually shown as single-stranded
with coding strand in 5’ to 3’ orientation
… so genetic code table can be used directly
Codon families
have 1 – 6
members
5’ …. AUG GGA UUG CCC CAC …. 3’
For the 61 sense codons, how many substitution mutations
are possible?
Genetic code is not “universal”
Some mitochondria, a few bacteria, a few protists
use a non-standard code
Table 1.4
Vertebrate mitochondrial code
UGA = Trp (instead of stop codon)
AUA, AUG = Met
AGA, AGG = stop codons
Possible implications of different codes in nature?
AMINO ACIDS – Venn diagram showing properties
Fig. 1.9
Amino acid substitution matrices
Amino acid substitutions:
Conservative
Ile
Radical
Cys
Table 4.7
BLOSUM62 matrix
- based on observed frequencies of amino acids
replacing other amino acids during protein evolution,
particularly within conserved regions
BLOSUM = BLOcks Substitution Matrix
www.doc.ic.ac.uk/