Download gene duplications

• Studying genetic mechanisms of change can
provide insight into large-scale evolutionary
change
• An organism’s genome is the full set of genes it
contains.
• In eukaryotes, most of the genes are found in the
nucleus, but genes are also present in plastids
and chloroplasts.
• Genes are shuffled in every generation of sexually
reproducing organisms via meiosis and
fertilization.
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• Studies of genomic evolution look at the genome
of an organism as an integrated whole and
attempt to answer questions such as:
– How do proteins acquire new functions?
– Why are the genomes of different organisms
so variable in size?
– How has the enlargement of genomes been
accomplished?
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The Evolution of Genome Size
• The size and composition of the genomes of many
species show much variation.
• Genome size varies greatly. Across broad
taxonomic categories, there is some correlation
between genome size and organism complexity.
• Multicellular organisms have more DNA than
single-celled organisms.
• Generally, more complex organisms have more
DNA than less complex organisms.
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Figure 26.8 A Large Proportion of DNA Is Noncoding
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The Evolution of Genome Size
If only the protein and RNA coding portions of
genomes are considered, there is much less
variation in size.
• Most of the variation in genome size is due to the
amount of noncoding DNA an organism has.
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Figure 26.7 Complex Organisms Have More Genes than Simpler Organisms
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Much of the noncoding DNA does not appear to have
a function.
But it can alter the expression of surrounding
genes.(regulatory genes)
Some noncoding DNA consists of pseudogenes
(duplicated genes which are nonfunctional).
Some consists of transposable elements (repetetive
DNA sequences that can move to different locations
in the genome)
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Nucleic acids or genes evolve when nucleotide
base substitutions occur.
Substitutions can change the amino acid
sequence, and thus the structure and function, of
the polypeptides.
By characterizing nucleic acid sequences and the
primary structures of proteins, molecular
evolutionists can determine how rapidly these
macromolecules have changed and why they
changed.
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Nucleotide substitutions may result in amino acid
replacements.
Change in the amino acid sequence can change the
charges, secondary and tertiary structure of a
protein, and thus its function.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• If an amino acid replacement does not make a
difference with respect to fitness, the two rates are
expected to be similar; the ratio would be close to
one.
• If an amino acid position is under strong stabilizing
selection pressure, the rate of synonymous
substitutions should be much higher than
nonsynonymous.
• If an amino acid position is under selection for
change, the rate of nonsynonymous substitutions
should be much higher than synonymous
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• The much slower rate of mutation at sites that do
affect molecular function is consistent with the
view that most nonsynonymous mutations are
disadvantageous and are eliminated from the
population by natural selection.
• In general, the more essential a molecule is for
cell function, the slower the rates of its evolution.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Evolutionary changes are determined by comparing
nucleotide or amino acid sequences among
different organisms.
The longer two sequences have been evolving
separately, the more differences they accumulate.
The timing of evolutionary changes can be
determined and causes can be inferred.
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Evolutionary Effects of Development Genes
• Genes that program development control the
rate, timing, and spatial pattern of changes in
an organism’s form as it develops into an adult
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Changes in Rate and Timing
• Heterochrony is an evolutionary change in the
rate or timing of developmental events
• It can have a significant impact on body shape
• The contrasting shapes of human and
chimpanzee skulls are the result of small
changes in relative growth rates
Animation: Allometric Growth
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Fig. 25-19
Newborn
2
5
Age (years)
15
Adult
(a) Differential growth rates in a human
Chimpanzee fetus
Chimpanzee adult
Human fetus
Human adult
(b) Comparison of chimpanzee and human skull growth
• Heterochrony can alter the timing of
reproductive development relative to the
development of nonreproductive organs
• In paedomorphosis, the rate of reproductive
development accelerates compared with
somatic development
• The sexually mature species may retain body
features that were juvenile structures in an
ancestral species
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 25-20
Gills
Changes in Spatial Pattern
• Substantial evolutionary change can also result
from alterations in genes that control the
placement and organization of body parts
• Homeotic genes determine such basic
features as where wings and legs will develop
on a bird or how a flower’s parts are arranged
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• Hox genes are a class of homeotic genes that
provide positional information during
development
• If Hox genes are expressed in the wrong
location, body parts can be produced in the
wrong location
• For example, in crustaceans, a swimming
appendage can be produced instead of a
feeding appendage
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• Evolution of vertebrates from invertebrate
animals was associated with alterations in Hox
genes
• Two duplications of Hox genes have occurred
in the vertebrate lineage
• These duplications may have been important in
the evolution of new vertebrate characteristics
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 25-21
Hypothetical vertebrate
ancestor (invertebrate)
with a single Hox cluster
First Hox
duplication
Hypothetical early
vertebrates (jawless)
with two Hox clusters
Second Hox
duplication
Vertebrates (with jaws)
with four Hox clusters
Changes in Genes
• New morphological forms likely come from
gene duplication events that produce new
developmental genes
• A possible mechanism for the evolution of sixlegged insects from a many-legged crustacean
ancestor has been demonstrated in lab
experiments
• Specific changes in the Ubx gene have been
identified that can “turn off” leg development
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 25-22
Hox gene 6
Hox gene 7
Hox gene 8
Ubx
About 400 mya
Drosophila
Artemia
Changes in Gene Regulation
• Changes in the form of organisms may be
caused more often by changes in the
regulation of developmental genes instead of
changes in their sequence
• For example three-spine sticklebacks in lakes
have fewer spines than their marine relatives
• The gene sequence remains the same, but the
regulation of gene expression is different in the
two groups of fish
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Concept 25.6: Evolution is not goal oriented
• Evolution is like tinkering—it is a process in
which new forms arise by the slight
modification of existing forms
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Evolutionary Novelties
• Most novel biological structures evolve in many
stages from previously existing structures
• Complex eyes have evolved from simple
photosensitive cells independently many times
• Exaptations are structures that evolve in one
context but become co-opted for a different
function
• Natural selection can only improve a structure
in the context of its current utility
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 25-24
Pigmented
cells
Pigmented cells
(photoreceptors)
Epithelium
Nerve fibers
(a) Patch of pigmented cells
Fluid-filled cavity
Epithelium
Optic
nerve
Nerve fibers
(b) Eyecup
Cellular
mass
(lens)
Pigmented
layer (retina)
(c) Pinhole camera-type eye
Cornea
Optic nerve
(d) Eye with primitive lens
Cornea
Lens
Retina
Optic nerve
(e) Complex camera-type eye
Concept 26.4: An organism’s
evolutionary history is
documented in its genome
Comparing nucleic acids or other molecules to
infer relatedness is a valuable tool for tracing
organisms’ evolutionary history
DNA that codes for rRNA changes relatively
slowly and is useful for investigating branching
points hundreds of millions of years ago
mtDNA evolves rapidly and can be used to
explore recent evolutionary events
Another way that genomes evolve is by gene
duplications. Copies may have one of four fates:
1.Both copies retain original function (more protein
product could be made).
2.Both copies retain original function but expression
diverges in different tissues or at different times.
3.One copy becomes nonfunctional from accumulation
of deleterious substitutions and becomes a
pseudogene.
4. One copy accumulates substitutions that allow it to
perform a new function.
Gene duplication may involve part of a gene, a single
gene, parts of a chromosome, or whole chromosomes.
Gene Duplications and Gene
Families
Gene duplication increases the number of genes
in the genome, providing more opportunities for
evolutionary changes
Like homologous genes, duplicated genes can be
traced to a common ancestor
Orthologous genes are found in a single copy in
the genome and are homologous between
species
They can diverge only after speciation occurs
Paralogous genes result from gene duplication,
so are found in more than one copy in the
genome
They can diverge within the clade that carries
them and often evolve new functions
Fig. 26-18
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Species A
Orthologous genes
Species B
(a) Orthologous genes
Species A
Gene duplication and divergence
Paralogous genes
Species A after many generations
(b) Paralogous genes
Genome Evolution
Orthologous genes are widespread and extend
across many widely varied species
Gene number and the complexity of an organism
are not strongly linked
Genes in complex organisms appear to be very
versatile and each gene can perform many
functions
Successive rounds of duplication and mutation can
result in gene families, such as the globin gene
family.
Amino acid sequencing of globins suggests they
arose via gene duplications
Concept 26.5: Molecular clocks
help track evolutionary time
To extend molecular phylogenies beyond the
fossil record, we must make an assumption
about how change occurs over time
Neutral Theory
Neutral theory states that much evolutionary
change in genes and proteins has no effect on
fitness and therefore is not influenced by
Darwinian selection
It states that the rate of molecular change in these
genes and proteins should be regular like a clock
The neutral theory of molecular evolution:
The majority of mutations are neutral, and accumulate
through genetic drift.
If a mutation confers an advantage, it quickly becomes
fixed in a population.
Using the rationale that the rate of fixation of mutation
is theoretically constant and equal to the neutral
mutation rate, the concept of the molecular clock
was developed.
The concept of the molecular clock states that
macromolecules evolving in different populations
should diverge from one another at a constant rate.
The number of changes in these molecules can
determine when the species diverged.
A molecule that illustrates this principle is the enzyme
cytochrome c, a component of the respiratory chain
in mitochondria.
Molecular Clocks
A molecular clock uses constant rates of
evolution in some genes to estimate the
absolute time of evolutionary change
In orthologous genes, nucleotide substitutions
are proportional to the time since they last
shared a common ancestor
In paralogous genes, nucleotide substitutions are
proportional to the time since the genes
became duplicated
Fig. 26-19
Molecular clocks are calibrated against branches
whose dates are known from the fossil record
90
60
30
0
0
60
30
90
Divergence time (millions of years)
120
Difficulties with Molecular Clocks
The molecular clock does not run as smoothly as
neutral theory predicts
Irregularities result from natural selection in which
some DNA changes are favored over others
Estimates of evolutionary divergences older than
the fossil record have a high degree of
uncertainty
The use of multiple genes may improve estimates
Applying a Molecular Clock: The
Origin of HIV
Phylogenetic analysis shows that HIV is
descended from viruses that infect
chimpanzees and other primates
Comparison of HIV samples throughout the
epidemic shows that the virus evolved in a very
clocklike way
Application of a molecular clock to one strain of
HIV suggests that that strain spread to humans
during the 1930s
Fig. 26-20
0.20
0.15
0.10
Computer model
of HIV
Range
0.05
0
1900
1920
1940
1960
Year
1980 2000