Evolution of Duplicated
Genomes
Talline Martins
4.24.07
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-DegenerationComplementation (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
z
PS = 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 DNAbinding site)
• How: used sites, fixed-sites, and branch
models in addition to Bayes
Results
FLO
DEF
1. DNA-binding
domain in FLO
and MADS
domain in DEF
are under
stronger purifying
selection than
other domains.
2. FLOB has
higher  than
FLOA in both
domains
3. DEF’s increase
in  is due to I, K,
and C-terminus
domains
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 coevolved (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 151:15311545.
• 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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