The origins & evolution of genome complexity

Seth Donoughe

Lynch & Conery (2003)

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

(contains all of its genes)

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.

Different kinds of diversity. How to infer about evolutionary past.

Increasing genome size

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 orders-of-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

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

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

• 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