Evolution of Duplicated Genomes

Talline Martins4.24.07

Possible Consequences of Polyploidization

Null hypothesis Interlocus gene conversion

Loss of homoeologue

Wendel, 2000

Genomic changes

• Many genome-level changes may occur as a result of genomic ‘shock’– Increased transposable element activity– Elevated levels of DNA methylation

• Homoeologous recombination• Inter-genomic concerted evolution• Non- and reciprocal translocations

Processes involved in diploidization

What happens to the duplicate genes that remain???

Persistence of Duplicate Genes

• Classical model:– The most common fate of duplicated genes is to become

null through deleterious mutations. The only mechanism for preservation of duplicate genes is through fixation of beneficial mutations (neofunctionalization).

• Problems with the classical model:– Fraction of genes preserved is higher than predicted– Evidence for purifying selection can be found in both loci– Relative lack of null alleles segregating in extant

populations

The Duplication-Degeneration-Complementation (DDC) Model

• Degenerative mutations facilitate rather than hinder the preservation of duplicate functional genes.– Duplicate genes lose different regulatory

subfunctions– They must complement each other to retain all

ancestral functions

Possible Fates of Duplicate Genes

Probability of Subfunctionalization

• The probability of maintenance of duplicate genes increases with number of number of regulatory elements

zPS = Σ PS,i

i=2

Complex Regulatory Regions

Why are some duplicates expressed in some tissues together but not in others?

Embedded and overlapping regulatory regions may reduce the number of subfunctions

Relaxed Selection Among Duplicate Regulatory Genes in Lamiales

LFY/FLO & AP3/DEF

Why are the duplicates still around?

• Role of selection

– Non-synonymous/synonymous substitution Dn/ds ()

– If < 1; purifying selection = 1; no selection (neutral) > 1; positive selection

Codon Substitution Models

• Branch and fixed-sites models• Sites and branch-site models

Branch and Fixed-Sites Models

• Branch models: Models R1-R4

• Fixed-sites model: compare ’s between paralogs– Model C (single )– Model E (allows

separate ’s for paralogs)

Results

LFY/FLO = paralogs diverging more quickly relative to single-copy lineages (R2) , and significantly different from each other (model E).AP3/DEF = paralogs diverging more quickly relative to single-copy lineages (R2), but not significantly different from each other (models C and E).

Sites and Branch-Sites Models(more powerful way to test for positive selection)

• Sites models: “hold constant among all branches while allowing to take on multiple values among site classes”– Models: M1a, M2a, M7, M8

• Branch-sites models: 1 set as foreground branches, allowing for different ’s over different branches and sites.– Reflects initial positive selection on duplicates

followed by purifying selection on ancestral lineages

– Model A and Model Anull. (2 is fixed at 1)

Results

Is different among functional domains of LFY/FLO & AP3/DEF?

• DEF: MADS (DNA-binding site), I, K, and C-terminus

• FLO: N- and C-terminus (putative DNA-binding site)

• How: used sites, fixed-sites, and branch models in addition to Bayes

Results 1. DNA-binding domain in FLO and MADS domain in DEF are under stronger purifying selection than other domains.

3. DEF’s increase in is due to I, K, and C-terminus domains

2. FLOB has higher than FLOA in both domains

FLO

DEF

Conclusions….• Continuous purifying selection on both

paralogs for both genes, although relaxed in comparison to single-copy taxa (supports the DDC model).

• Relaxed constraint in some domains may be an indication of subfunctionalization.– Subfunctionalization rather than adaptive

evolution contributes to preservation of duplicate genes

Alternative explanations

• Gene Dosage– Unlikely, because duplicates have diverged

and because of partial functional redundancy

• Transcriptional regulatory interactions– FLO and DEF paralogs may have co-

evolved (concerted divergence)– Still needs to be tested

References• Chen, ZF and Z Ni. 2006. Mechanisms of genomic

rearrangements and gene expression changes in plant polyploids. BioEssays 28:240-252.

• Adams, KL and JF Wendel. 2005. Polyploidy and genome evolution in plants. Curr. Op. Plant Bio. 8:135-141

• Wendel JF. 2000. Genome evolution in polyploids. Plant Mol. Bio. 42:225-249.

• Force et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.

• Aagard JE, Willis JH, and PC Phillips. 2006. Relaxed selection among duplicate floral regulatory genes in Lamiales. J Mol. Evol. 63:493-503.

Time to Subfunctionalization

Fates of duplicated genes are determined shortly after polyploidization

Ratio of mutation rate in regulatory and coding regions is a weak factor in expected degree of resolution

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