the origins & evolution of genome complexity seth donoughe lynch & conery (2003)
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The origins & evolution of genome complexity
Seth Donoughe
Lynch & Conery (2003)
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Plan of attack
• Review simplified definitions for: genes, genome, mRNA, codons, introns/exons, transposons– Two-fold purpose
• Work through the data, discussing the theory along the way
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Gene: An inheritable sequence of DNA, which encodes one or more products.
Genome: All of the hereditary information encoded in an organism’s DNA
(contains all of its genes)
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DNA is transcribed into single-stranded mRNA.
(with A, U, G, and C as the nucleotides)
Each set of three nucleotides forms a codon.
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RNA polymerase
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The “canonical” genetic code. What are “silent sites”?
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mRNA is translated into a chain of amino acids = protein.
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Different kinds of diversity. How to infer about evolutionary past.
Increasing genome size
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Increasing genomic complexity in eukaryotes over evolutionary time.
1) Introns (and exons)
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Increasing genomic complexity in
eukaryotes over evolutionary time.
2) Transposons
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2) Transposons
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What caused this increase in genomic size and complexity?
• The evolution of single-celled eukaryotes and multicellularity brought:– Increased intracellular structural variety– Cell differentiation and specialization
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Perhaps genomic complexity evolved as a means to achieve this adaptive diversification.
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But there are problems with this hypothesis...
• Genomic complexity is not the only way to create different functions from the same genes
• Some (rare) prokaryotes are capable of cell differentiation with smaller genomes
• Increasingly long introns in some multicellular organisms and many transposons do not bring a clear functional advantage.
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Alternative hypothesis
“The transition from prokaryote to unicellular eukaryote to multicellular eukaryotes was associated with orders-of-magnitude reductions in population size”
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Alternative hypothesis
As population size decreased, genetic drift became an increasingly powerful factor in changing the features of the genome. Why?
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Genetic Drift
20 alleles
Initial freq. = 0.5
In general, alleles drift to fixation (frequency of 0 or 1) significantly faster in smaller populations.
N = 10
N = 100
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What is the [evolutionarily] meaningful size of a population?
• Abundance is a coarse measurement
• There is a broad trend:– Inverse relationship between population
density and the body mass of an individual
• We can do better with: – genetic effective population size.
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Effective population size (Ne)
• How “faithfully” gene frequencies are transmitted across generations.– Can be estimated from the rates of mutation at
silent sites (read: neutral mutations).
– # of neutral mutations = 4Neu
– Where u is the mutation rate per nucleotide
• We can roughly measure u independently for taxa, allowing us to estimate Ne
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How does smaller Ne lead to genome complexity?
• Gene duplication occurs at roughly the same rate (probably due to the same mechanism across all taxa) but …
• Duplicated genes are lost much more slowly in smaller populations
• Pairs of partially degenerated genes can fulfill a single function
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Duplication
• Duplicated genes can acquire new beneficial functions but the findings of this study indicate that this is unlikely to have been the driving cause behind increased genomic complexity.
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Increasing genomic complexity over evolutionary time
• Introns and exons– Origin unknown, probably in the single ancestor of
eukaryotes– Average of 4-7 introns per multicellular organism
gene– Average of 2 for unicellular eukaryote gene
• Virtually none has been found in prokaryotes
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Sources and image credits
• http://216.218.133.62/img/Pictures/codon_wheel.jpg• http://bioephemera.com/wp-content/uploads/2007/03/codon%5B1%5D.gif• http://undergrowth.org/system/files/images/tree-of-life-colour.preview.jpg• http://mgl.scripps.edu/people/goodsell/pdb/pdb40/1i6h-composite.gif• http://en.wikipedia.org/wiki/Image:Phylogenetic_tree.svg• http://upload.wikimedia.org/wikipedia/commons/0/07/Gene.png• http://upload.wikimedia.org/wikipedia/commons/1/17/Pre-mRNA_to_mRNA.png• http://upload.wikimedia.org/wikipedia/commons/thumb/f/fe/
PLoS_Mu_transposon_in_maize.jpg/491px-PLoS_Mu_transposon_in_maize.jpg• http://upload.wikimedia.org/wikipedia/commons/d/d4/Cell_differentiation.gif• http://en.wikipedia.org/wiki/Genetic_drift