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Evolutionary change involves genetic change
Phenotype
Genotype
• Study of evolution of macromolecules- nature of changes (in DNA, protein) & their impact
BIO 3102 MOLECULAR EVOLUTION
M.C. Escher “Sky & water”
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cenancestor - most recent common ancestor of extant organisms
extinct lineages
primordial life form
modern species
Brown Fig.16.1
• Use of molecular data to help reconstruct evolutionary history- phylogenetic trees
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Ottawa Citizen December 3, 2010
Science December 2, 2010
Building blocks of DNA, proteins & lipids (for life on earth)
carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur
Nature December 9, 2010
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www.csmt.ewu.edu/.../ chem163/163LT1.html
Closely-related organisms have moresimilar protein sequences thandistant organisms
MOLECULAR CLOCKS
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“Taking an axe to the Tree of Life...”
“... far more complex scenario than Darwin could have imagined...
“Web-of-life”
Dalhousie University News July 11, 2007
Ford Doolittle
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
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2. Is the frog more closely related to the fish or to the human, based on this tree?
1. Which tree is more accurate?
“The tree-thinking challenge” Science 310:979, 2005
A B
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Volpe & Rosenbaum Fig.14.3
Schopf PNAS 91:6735, 1994
Extant
Fossil
Fossil
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Mass extinctions, as well as radiations leading to taxonomic diversity
App1.Fig.2
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“Loss and recovery of wings in stick insects”Nature 421: 264, 2003
Winged
Partiallywinged
Wingless
Morphological data Phylogeny based on molecular data
Male Female
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GENE
- sequence of DNA (or RNA) that is essential for a specific function
EVOLUTIONARY INFORMATION FROM DNA SEQUENCES?
1. Protein-coding genes
2. RNA-specifying genes
- structural
- regulatory
U.S. Dept of Energy Human Genome Program, http://www.ornl.gov/hgmis
Do not use term in text (p.9): “Untranscribed genes” for #3
3. Functional DNA elements
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PSEUDOGENE
- non-functional DNA with high degree of similarity to afunctional gene
How can pseudogenes arise during evolution?
“SILENT” GENE
- untranscribed, but potentially functional at DNA level
Orthologous genes
- descendants of an ancestral gene that was presentin the last common ancestor of two or more species
Paralogous genes
- arose by gene duplication within a lineage
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Fig.1.4
“TYPICAL” EUKARYOTIC PROTEIN-CODING GENE
Is there an error in this figure?
Where is the promoter? 5’ UTR ? 3’ UTR ?
What regions will be present in the mRNA?
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“TYPICAL” BACTERIAL GENE ORGANIZATION
Fig.1.6
Operon = cluster of co-transcribed genes
How many promoters in this region?
How many proteins encoded?
Evolutionary advantages of operon organization?
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- DNA usually shown as single-stranded with coding strand in 5’ to 3’ orientation
PROTEIN-CODING GENES
5’ …. AUG GGA UUG CCC GCC …. 3’
3’ .… TAC CCT AAC GGG CGG …. 5’
5’ …. ATG GGA TTG CCC GCC …. 3’ “coding strand”DNA
“template strand”
mRNA
… so genetic code table can be used directly
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Codon families have 1 – 6 members
5’ …. AUG GGA UUG CCC CAC …. 3’
For the 61 sense codons, how many substitution mutations are possible?
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Genetic code is not “universal”
Some mitochondria, a few bacteria, a few protistsuse a non-standard code
Table 1.4 Vertebrate mitochondrial code
UGA = Trp (instead of stop codon)
AGA, AGG = stop codons
AUA, AUG = Met
Possible implications of different codes in nature?
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AMINO ACIDS – Venn diagram showing properties
Fig. 1.9
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Table 4.7
Conservative
Ile
Amino acid substitutions:
Radical
Cys
Amino acid substitution matrices
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BLOSUM62 matrix
www.doc.ic.ac.uk/
- based on observed frequencies of amino acids replacing other amino acids during protein evolution, particularly within conserved regions
BLOSUM = BLOcks Substitution Matrix
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