Evolution by polyploidy

Dan Graur
Polyploidy = the addition of one or more complete sets of
chromosomes to the original set.

two copies of each autosome = diploid

four copies of each autosome = tetraploid
six copies of each autosome = hexaploid

The gametes of diploids are haploid, those of tertraploids are diploid,

those of hexaploid are triploid, and so on.

Organisms with an odd number of autosomes, e.g., the domestic

banana plant (Musa acuminata), cannot undergo meiosis or reproduce
sexually.

Musa barbisiana (diploid) Musa acuminata (triploid)

Two main types of polyploidy:
autopolyploidy (genome doubling) = the
multiplication of one basic set of
chromosomes
allopolyploidy = the combination of
genetically distinct, but similar chromosome
sets.

Autopolyploids are derived from within a

single species; allopolyploids arise via
hybridization between two species.
autopolyploidy

4
 autopolyploidy
Autopolyploidy may be common in
plants, although its prevalence may be
underestimated in the taxonomic
literature.
One species that is
doubtlessly a true
autopolyploid, rather
than an allopolyploid derived from two
very similar diploids, is the potato,
Solanum tuberosum 5
 autopolyploidy
Advantage of autopolyploidy:

1.Much higher levels of heterozygosity than do

their diploid progenitors due to polysomic
inheritance
2.Maintenance of more than two alleles per locus,
allowing them to produce a larger variety of
allozymes than diploids
3.Larger effective population sizes than diploids,
allowing selective processes to be much more
effective relative to random genetic drift.
6
 autopolyploidy
Much higher levels of heterozygosity than do their
diploid progenitors due to polysomic inheritance

• Let us consider, for example, an autotetraploid (aabb) derived

from a heterozygous diploid (ab).
• Assuming simple tetrasomic inheritance, the genotype aabb is
expected to produce diploid gametes in the ratio 1aa:4ab:1bb.
• In the progeny, the ratio of the genotypes will be
1aaaa:8aaab:18aabb:8abbb:1bbbb.
• That is, heterozygotes (aaab, aabb, abbb) are expected to
outnumber homozygotes (aaaa, bbbb) 17 to 1.
• In comparison, in diploids the heterozygote to homozygote ratio
is 1:1.
7
 autopolyploidy
Disadvantages of autopolyploidy:

(1) prolongation of cell division time

(2) increase in the volume of the nucleus
(3) increase in the number of chromosome disjunctions
during meiosis
(4) genetic imbalances
(5) interference with sexual differentiation when the sex
of the organisms is determined by either the ratio
between the number of sex chromosomes and the
number of autosomes (as in Drosophila), or by degree of
ploidy (as in Hymenoptera).

8
allopolyploidy

9
Allopolyploidy is much more common in
nature than autopolyploidy. About 80% of all
land plants may be allopolyploids.

Red circles indicate instances of

allopolyploidy.
The blue circle indicates an
instance of autopolyploidy.
The green square indicates a
putative triplication event before
the divergence among
dicotydelons.
The two black ovals indicate an
ancestral angiosperm genome
duplication (190-230 million years
ago) and an ancestral seed-plant
duplication (320-350 million years
ago).
 Triticum urartu (AA)  Aegilops speltoides (BB)

T. turgidum (AABB)  T. tauschii (DD)

The common bread wheat

(Triticum aestivum) is an
allohexaploid containing three
distinct sets of chromosomes
derived from three different
T. aestivum (AABBDD)
diploid species of goat-grass
(Aegilops) through a tetraploid
intermediary (durum wheat).
11
In animals, allopolyploidy is rare. Allopolyploidy was found in insects,
fish, reptiles, and amphibians. For example, Xenopus laevis, the
African clawed frog of laboratory fame, is an allotetraploid. No cases
of polyploidy have ever been found in birds. Two mammalian species
are suspected tetraploids, the red vizcacha rat (Tympanoctomys
barrerae) and the golden vizcacha rat (Pipanacoctomys aureus),
however, some disagreement exists in the literature.

4N = 100 + XY
Consequences of polyploidy

At a phenotypic level, the effects of polyploidization are often mild.

In many cases, polyploidy seem to have almost no effect on the
phenotype. For example, diploid, autopolyploid, and allopolyploid
Chrysanthemum species vary in chromosome number from 18 to
198, yet they are almost indistinguishable from one another. Similar
observations have been made in roses (Rosa), leptodactylid toads
(Odontophrynus), and goldfish (Carasius).
A tale of two daisies
Haplopappus gracilis (yellow spiny daisy) = 4 chromosomes

Senecio roberti-friesii (Robert & Friesi’s groundsel,

belongs to the daisy family) = 90 chromosomes
Consequences of polyploidy

Cell volume generally rises with increasing genome size, although

the exact relationship between ploidy and cell volume varies among
environments and among taxa.
Although average cell size is larger in polyploids, the size of the
adult polyploidy organism may not be altered.
As a rough generalization, polyploidization is more likely to increase
adult body size in plants and invertebrates than in vertebrates.
The poor correlation between cell size and organismal size was even
remarked upon by Albert Einstein, who stated:
“Most peculiar for me is the fact that in spite of
the enlarged single cell, the size of the animal is
not correspondingly increased.”
Following polyploidization, all genes become
duplicated = OHNOLOGS
An important feature of many newly formed
polyploids is that their genomes are unstable and
undergo rapid repatterning and segmental loss.

The rapidity of gene loss is illustrated by the bread

wheat, Triticum aestivum, an allohexaploid that may
have originated as early as 10,000 years ago.

In this very short time, many of the

triplicated loci have been silenced. It has
been estimated that the proportion of
enzymes produced by triplicate, duplicate,
and single loci in wheat is 57%, 25%, and
18%, respectively.
Sometimes duplicates persist for long periods
of time

~8% of duplicated genes have remained in

yeast about 100 million years following
allotetraploidization.

~77% of ohnologs are still detectable in

Xenopus laevis about 30 million years after
allotetraploidization.
Consequences of polyploidy (continued)

Transposable elements that had been repressed within each parent

lineage may be activated in hybrids, and can facilitate the movement
of genes and promote unequal crossing over.

Polyploidy is an important factor in speciation. In particular, sexually

reproducing autotetraploids are automatically isolated from their
diploid progenitors because they produce diploid gametes; were
these to combine with the haploid gametes of the diploids, they
would give rise to triploid progeny.
Consequences of polyploidy (continued)

Stebbins (1971) postulated that polyploids represent dead ends

because of the inefficiency of selection when deleterious alleles can
be masked by multiple copies.
Mayrose et al. (2011) provided quantitative corroboration of the
dead-end hypothesis by showing that speciation rates of polyploids
are significantly lower than those of diploids, and their extinction
rates are significantly higher.

G. Ledyard Stebbins Sally Otto

• Diploidization is the evolutionary process whereby a tetraploid species “decays” to become
a diploid with twice as many distinct chromosomes.
• The key event in diploidization is the switch from having four chromosomes that form a
quadrivalent at meiosis, to having two pairs of chromosomes each of which forms a bivalent.
• In population-genetics terms, this is the switch from having four alleles at a single locus
(tetrasomic inheritance) to having two alleles at each of two distinct loci (disomic
inheritance).
A newly created polyploid = Neopolyploid

Polyploid after diploidization = Paleopolyploid

(diploid ancestors unknown or extinct) or
Mesopolyploids (diploid ancestors known and
extant)

Cryptopolyploid (literally, a hidden polyploid) =

an ancient polyploid that is no longer
distinguishable from a diploid.
Distinguishing between gene duplication and
genome duplication

Most genomes contain gene duplications.

They can either be the result of gene duplication or

whole genome duplications.

How can one distinguish between the two

mechanisms?
Expectation: Following polyploidization, all the paralogous genes in
the genome (ohnologs) should each yield the same tree (b). If,
however, the paralogous genes yield alternative trees (c or d), then it
is unlikely that all the gene duplications occurred at the same time.

polyploidy
Regions of Double Synteny

Two or more genomic regions

containing paralogous arrays of
genes.
Is Saccharomyces cerevisiae a cryptotetraploid?

Wolfe and Shields (1997) searched the complete yeast

proteome for regions of double synteny.

The criteria used for defining two regions as duplicated were:

(1) a sequence similarity between the two regions associated

with a probability of less than 10–18 of it being fortuitous
(2) at least three protein-coding genes or open-reading frames in
common, with intergenic distances of less than 50 Kb
(3) conservation of gene order and orientation of the genes
relative to the centromere.
54 nonoverlapping pairs of
duplicated regions
spanning about 50% of the
yeast genome.

~900 of the ~5,800 genes in

the yeast genome, are
paralogs located in
duplicated chromosomal
regions (blocks of doubly
conserved synteny or
paralogons). 27
2 possible explanations:
(1) the duplicated regions were formed
independently by regional duplications
occurring at different times.
(2) the duplicated regions have been
produced simultaneously by a single
tetraploidization event, followed by
genome rearrangement and loss of
many redundant duplicates. 28
50/54 duplicated regions have
maintained the same orientation
with respect to the centromere.

54 independent regional
duplications are expected to result
in ~7 triplicated regions (i.e.,
duplicates of duplicates), but none
was observed. 29
Loss of 92% of
the duplicate
genes.

Occurrence of
70-100 map
disruptions.
30
The expected genomic signature of whole genome duplication:

Following duplication, sister regions would undergo gene loss by deletion; one or the other
of the two paralogous copies of each gene would be lost in most cases, with both paralogs
being retained only very rarely. Eventually, the only residual signature to show that two
regions arose from ancestral duplication is the presence of a few paralogous genes in the
same order and orientation scattered amidst a multitude of unrelated genes.
Close up to one example:
 Vertebrate polyploidy? The 2R hypothesis

A simple expectation of the 2R hypothesis:

In the absence of any gene duplications prior,

in between, or subsequent to the two rounds
of genome duplication, the expectation is an
(AB)(CD) topology, where A, B, C, and D are
paralogous genes (a). Any other topology (b,c)
may be interpreted as a refutation of the 2R
hypothesis.
 Vertebrate polyploidy? The 2R hypothesis

Out of the 92 resolved phylogenetic

topologies, only 22 topologies (24%) supported
the 2R hypothesis.
Out of the 53 phylogenies in which all internal
branches received statistically significant
support, only 11 topologies (21%) supported
the 2R hypothesis, leading the authors to
reject the hypothesis.
 Vertebrate polyploidy? The 2R hypothesis

The previous test was very strict.

If one selects only those human paralogs that have
duplicated before divergence of tetrapods from the
bonny fishes, the 2R hypothesis cannot be rejected.
Moreover, molecular clock analyses of all protein
families in humans that have orthologs in Drosophila
and C. elegans indicated that a burst of gene
duplication activity (polyploidization?) took place
350–650 million years ago.
A cryptooctoploid (Homo sapiens) and a
cryptosedectoploids (Cyprinus carpio)?

36