Transcript The origins and evolution of genome complexity

The origins &
evolution
of genome
complexity
Lynch & Conery (2003)
Seth
Donoughe
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
Gene: An inheritable
sequence of DNA, which
encodes one or more
products.
Genome: All of the hereditary
information encoded in an
organism’s DNA
DNA is transcribed into single-stranded mRNA.
(with A, U, G, and C as the nucleotides)
Each set of three nucleotides forms a codon.
RNA polymerase
The “canonical” genetic code. What are “silent sites”?
mRNA is translated into a chain of amino acids = protein.
Increasing
genome size
Different kinds of diversity. How to infer about evolutionary past.
Increasing genomic complexity in eukaryotes over
evolutionary time.
1) Introns (and exons)
Increasing genomic
complexity in
eukaryotes over
evolutionary time.
2) Transposons
2) Transposons
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
Perhaps genomic complexity evolved as a means to achieve this
adaptive diversification.
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.
Alternative hypothesis
“The transition from prokaryote to
unicellular eukaryote to multicellular
eukaryotes was associated with ordersof-magnitude reductions in population
size”
Alternative hypothesis
As population size decreased, genetic
drift became an increasingly powerful
factor in changing the features of the
genome. Why?
Genetic Drift
N = 10
20 alleles
Initial freq. = 0.5
In general, alleles
drift to fixation
(frequency of 0 or
1) significantly
faster in smaller
populations.
N = 100
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.
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
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
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.
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
Sources and image credits
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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_transposo
n_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