Sources of variation – Chapter 5
What we will cover:
• Kinds of Variation
• Where new alleles come from
• Where new genes come from
• Rates of mutation
Manute Bol 7' 7"
Muggsy Bogues 5’3”
Shawn Bradley 7’6” -barefoot
Kinds of Variation
1. Genetic
2. Environmental
3. Genotype x environment interaction
Kinds of Variation
1. Genetic
• The Machinery of Life
• Genetic Variation
1. Environmental
2. Genotype x environment interaction
Environmental Variation – Phenotypic plasticity
Phenotypic plasticity – when an
individuals phenotype is
influenced by the environment.
Representative examples of environmentally
induced alternative phenotypes
(polyphenism). (a) Normal (left) and
predator-induced (right) morphs of water
fleas, Daphnia cucullata (photo courtesy of
Ralph Tollrian); (b) wet-season (top) and dryseason (bottom) gaudy commodore
butterflies, Precis octavia (photo courtesy of
Fred Nijhout); (c) omnivore (top) and
carnivore-morph (bottom) spadefoot toad
tadpoles, Spea multiplicata (photo by David
Pfennig); (d) small-horned (left) and largehorned (right) dung beetles, Onthophagus
nigriventris (photo by Alex Wild); (e) broad,
aerial leaves and narrow, submerged leaves
(circled) on the same water crowfoot
plant, Ranunculus aquatilis (photo by John
Crellin/FloralImages).
David W. Pfennig , Matthew A. Wund , Emilie C. Snell-Rood , Tami Cruickshank , Carl D. Schlichting , Armin P. Mocz...
Phenotypic plasticity's impacts on diversification and speciation
Trends in Ecology & Evolution, Volume 25, Issue 8, 2010, 459 - 467
http://dx.doi.org/10.1016/j.tree.2010.05.006
Environmental Variation – Phenotypic plasticity
Induction of the “crown of thorns” in the D. atkinsoni species complex exposed to chemical
cues released by Triops cancriformis.
Inducible defense
Tadpole shrimp
Induction of the “crown of thorns”
in the D. atkinsoni species
complex exposed to chemical cues
released by Triops cancriformis.
This notostracan is portrayed on
an Austrian stamp as “the most
ancient extant animal species”. (A)
Induced Daphnia show a distinctly
enlarged carapace extension into
the head shield, forming heartshaped lobes lined with strong
spines (B: lineage 1, whole body
SEM image; C Left: lineage 3,
head). Noninduced individuals
exhibit inconspicuous lobes
without thorns (C Right: identical
clone of lineage 3)
"Triops cancriformis2" by Stijn Ghesquiere at the English language
Wikipedia. Licensed under CC BY-SA 3.0 via Wikimedia Commons http://commons.wikimedia.org/wiki/File:Triops_cancriformis2.jpg#media
viewer/File:Triops_cancriformis2.jpg
Phenotypic plasticity – when an
individuals phenotype is
influenced by the environment.
©2009 by National Academy of Sciences
Petrusek A et al. PNAS 2009;106:2248-2252
Predator cue induction experiments.
Lineage #3
Lineage #1
Petrusek A et al. PNAS 2009;106:2248-2252
©2009 by National Academy of Sciences
Environmental Variation
Examples of phenotypic plasticity abound.
Are they important to the process of evolution?
Experiments are with Daphnia clones, which are genetically identical.
Since Daphnia are genetically identical, the presence of a “crown of thorns” (or neck
teeth in textbook) is not passed on by genes from one generation to the next.
The trait is determined by the environment (the presence of a substance – a
kairomone).
A chemical released into the environment that benefits the receiver, but
What is a kairomone? has either a neutral or negative impact on the emitter.
Genotype by Environmental Interactions
Why are environmentally induced traits interesting from an evolutionary standpoint?
Because phenotypic plasticity is a heritable trait
An organism that develops different phenotypes in different environments is said to
exhibit phenotypic plasticity.
Genotype by Environmental Interactions
In Leopard geckos (Eublepharis macularius), the sex of the offspring is determined by the
incubation temperature of the eggs.
Genotype by Environmental Interactions
The sex (sex ratio in this study) varies among males.
Reaction Norm – The pattern of phenotypes an
individual (genotype) may
develop upon exposure to
different environments.
% males
Multiple reaction
norms.
Different paternal families (n = 12) respond differently to incubation temperature.
Genotype by Environmental Interactions
A heat shock shortly before molting produces larvae of tobacco hornworm (Manduca sexta)
of different shades of black -> green.
Genotype by Environmental Interactions
Because the degree to which a phenotype responds to the environment is genetically
controlled, phenotypic plasticity can be selected for.
Selection for different degrees of
plasticity…
…results in lineages with
different reaction norms.
Genotype by Environmental Interactions
Because the degree to which a phenotype responds to the environment is genetically
controlled, phenotypic plasticity can be selected for.
Selection for different degrees of
plasticity…
…results in lineages with
different reaction norms.
Because phenotypic plasticity is a heritable trait, it forms the raw
material for evolution to act on.
Where New Alleles Come From
Mutation – An error in the replication of a nucleotide sequence, or any other alteration of
the genome that is not manifested as reciprocal recombination.
Where New Alleles Come From
Basic mutations in alleles come from errors in the DNA that escape repair before or during
replication.
Errors made during replication may go uncorrected, and may escape repair afterward.
Where New Alleles Come From
A mutation (spontaneous deamination) to the DNA that is not repaired during replication.
Where New Alleles Come From
A mutation (spontaneous deamination) to the DNA that is not repaired during replication.
Will become fixed if it is not
repaired before the next
replication.
A permutation – an alteration still susceptible to repair.
Where New Alleles Come From
Point mutations can be classified by the type of change to the DNA sequence
transitions = replace purine with purine (A for G), pyrimidine with pyrimidine (T for C).
transversions = replace purine with pyrimidine (T for G) and vice-versa.
Transitions are 2x more
common than transversions.
Where New Alleles Come From
Point mutations can be classified by the type of change to the DNA sequence
transitions = replace purine with purine (A for G), pyrimidine with pyrimidine (T for C).
transversions = replace purine with pyrimidine (T for G) and vice-versa.
Transitions are 2x more
common than transversions.
Purines
Pyrimidines
Where New Alleles Come From
Fitness effects of point mutations - Overall, the effect of a point mutation can range from
highly beneficial to very harmful (deleterious).
Where New Alleles Come From
Replacement substitution
(nonsynonymous, or missense) –
a base substitution that causes a
change in the amino acid.
Where New Alleles Come From
Silent site substitution
(synonymous) – a base
substitution that does not cause
a change in the amino acid due
to codon redundancy.
• Because of the structure of the
genetic code, most synonymous
mutations occur in the third
base position of the codon.
• Approximately 70% of changes
in the third position are
synonymous, whereas all
changes in the second, and
most (96%) at the first position
are meaningful
(nonsynonymous).
Where New Alleles Come From
Nonsense mutation -
Where New Alleles Come From
A frameshift mutation. This
changes the reading frame, so all
codons after the point of
mutation are affected:
Most frameshift mutations will
have large effects – usually
negative.
It is fairly common for frameshift
to result in premature stop
codon (nonsense mutation) – so
resulting protein may be
completely non-functional.
Where New Alleles Come From
A frameshift mutation. This
changes the reading frame, so all
codons after the point of
mutation are affected:
a. additions = extra base
inserted
b. deletions = base is “missed”
These collectively are known as
indels.
(indel = insertions + deletions)
Where New Alleles Come From
The fitness effects of a mutation will also depend on environmental conditions as well.
e.g.: sickle-cell anemia.
Where New Genes Come From
Alterations of the karyotype fall into two major categories:
• Rearrangements of one or more chromosomes. These are caused by breaks in
the chromosome, followed by rejoining of the pieces in new configurations.
• Changes in the number of wholes sets of chromosomes – polyploidy.
A karyotype (from Greek κάρυον karyon, "kernel,
seed or nucleus", and τύπος typos, "general
form") is the number and appearance of
chromosomes in the nucleus of a eukaryotic
cell.(Wikipedia)
Often described as a picture of an individual’s
chromosomes.
Where New Genes Come From
Chromosome rearrangements include:
• Deletions or deficiencies
• Inversions
• Duplications
• Translocations
• Fissions and fusions
Where New Genes Come From
Gene Duplications - are either short or long segments of extra chromosome
material originating from duplicated sequences within a genome.
Unequal crossing over – an error during
genetic recombination (meiosis) when two
chromosomes are not perfectly aligned.
The incorrect alignment can occur when a
transposable element has been inserted at
multiple loci.
Transposable element (transposons) – Any DNA sequence
capable of transmitting itself or a copy of itself to a new
location in the genome.
Where New Genes Come From
Gene Duplications – Unequal crossing over
The globin gene family = two clusters of loci coding for component
subunits of hemoglobin:
α-like cluster on chromosome 16 includes 3 functional loci
β-like cluster on chromosome 11 includes 5 functional loci
• Each locus codes for a polypeptide (protein
subunit) of hemoglobin.
• Two of the protein subunits come from the αlike cluster and two of the protein subunits
come from the β-like cluster.
• Each locus is expressed during a different time
in human development– functions differ
enough to make each locus well-adapted for a
different stage of development
Where New Genes Come From
Each locus is expressed during a different time in human development– functions
differ enough to make each locus well-adapted for a different stage of development.
Test hypothesis that the loci within the gene cluster arose via duplication.
Prediction #1 = should get fairly
high degree of structural and
functional similarity.
3 lines of evidence support the
hypothesis:
Where New Genes Come From
Prediction #1 = should get fairly high degree of structural and functional similarity.
3 lines of evidence support the hypothesis:
1) high structural similarity of
transcription units among
loci, including position and
length of introns and exons
2) high sequence similarity
among loci
3) similarity in function
Where New Genes Come From
Prediction #2: Not all duplicated genes will have
accumulated favorable mutations – should see
some loci that are non-functional (“failed
experiments”).
Supported by presence of pseudogenes =
non-functional lengths of DNA (but with
some structural similarities)
Where New Genes Come From
Prediction #2: Not all duplicated genes will have
accumulated favorable mutations – should see
some loci that are non-functional (“failed
experiments”).
Supported by presence of pseudogenes =
non-functional lengths of DNA (but with
some structural similarities)
Where New Genes Come From
Gene Duplications – Retroposition (retroduplication)
Occurs when processed messenger RNA
(lacking introns) is reverse transcribed to form
DS-DNA.
If the new DS-DNA is inserted into a
chromosome, it becomes a duplicate gene
(pseudogene).
Often non-functional because the new
segment of DNA lacks the nearby regulatory
sequences that cause it to be transcribed.
Where New Genes Come From
Gene Duplications – Footprints in the genome
Genes created by unequal crossing over:
• Contain the same introns as the parental genes.
• Found in tandem on the same chromosome.
Genes created by retroposition:
• Lack introns.
• Found far from original gene.
Where New Genes Come From
Chromosome mutations
• Inversions
• Genome duplication
Where New Genes Come From
Chromosome mutations
Inversions – when a chromosome segment
breaks in two places and reanneals with the
internal segment reversed.
Individual organisms may be homozygous or
heterozygous for a rearranged chromosome.
Homokaryotype – both chromosomes are
affected.
Heterokaryotype – only one chromosome is
affected.
Where New Genes Come From
Chromosome mutations
Inversions affect the degree
of linkage among alleles.
linkage = tendency of alleles
to be inherited together.
Where New Genes Come From
Inversions generally lower the
recombination frequency
within the inverted sequence,
because crossing over within
such sequences in
heterozygotes
requires ‘looping’, and this can
lead to chromosomal
abnormalities.
Genes in the loop tend to
remain together as a
nonrecombinant block, called a
supergene.
Where New Genes Come From
Homokaryotypes can cross-over
normally and gamete formation
is unaffected, but…
…in heterokaryotypes,
fertility may be reduced because
many gametes are inviable
because the chromosome lacks a
centromere
Other chromosomes are missing
genetic information, and are also
inviable.
Where New Genes Come From
Chromosome mutations
Genome duplication – duplication of entire sets of chromosomes.
Occurs as an error during:
Meiosis I
Meiosis II
Failure to separate
Failure to segregate
Offspring are polyploidy through self-fertilization with diploid gametes.
Where New Genes Come From
Euploid variation- an entire set of chromosomes is duplicated once or
several times.
Since most reproducing eukaryotes are diploid, with two sets of chromosomes (2n),
euploid variations may extend from the haploid or monoploid condition (1n) to various
levels of polyploidy.
Where New Genes Come From
How polyploids develop
Autopolyploidy - the appearance
of extra sets of chromosomes
within a species itself.
Common in plants – mosses,
apples, pears, bananas,
tomatoes, corn
Where New Genes Come From
How polyploids develop
Allopolyploidy- polyploids that
originate from crossing
between different species.
Appears in such plants as wheat.
Where New Genes Come From
Polyploidy is common among plants. Estimates of the proportion of
polyploidy angiosperms ranges from 30% to 50-70%.
a. Polyploid formation in plants is very high – possibly as high as the rate of
point mutations.
b. Majority of polyploidy plants are allopolyploids (from closely related
species) and they usually present a mixture of traits or an intermediate
condition of their parents.
Where New Genes Come From
Polyploidy is much rarer in animals than in plants, because animals show
much greater developmental sensitivity to even a small change in
chromosome number.
Maintaining the same proportions of X and Y chromosomes present in normal
diploids is difficult for animals.
Males which are XY and females are XX could lead to establishment of
XXYY males and XXXX females.
The subsequent combination of gametes produced by these individuals
(XY sperm + XX eggs) might produce XXXY individuals that are not completely
female or male.
Where New Genes Come From
Kleinfelter’s syndrome
Turner’s syndrome
Where New Genes Come From
Aneuploid variation – the abnormal
condition were one or more
chromosomes of a normal set of
chromosomes are missing or present
in more than their usual number of
copies.
E.g. if an otherwise diploid organism
has three copies of one its
chromosomes -> Down’s syndrome.
Down’s syndrome
Trisomy at chromosome #21.
When animal polyploidy species do occur, they
usually have some form of asexual
reproduction, such as parthenogenesis
(embryonic development of eggs without
fertilization).
Where New Genes Come From
Huge amounts of duplication in the humane
genome.
- ~5% consists of copies longer than 1,000
bp.
- ½ chromosome 20 recurs in a rearranged
state on chromosome 18.
- A large block of chromosome 2’s short arm
appears as ¾ of chromosome 14 ,
and a section of its long arm appears on
chromosome 12.
Measuring Genetic Variation in Natural Populations
Mean heterozygosity = % of heterozygous loci in the average individual.
1. Measure variation across loci within an individual,
2. Then averaged across population
1) AaBbCCDD
2) AABBCCDD
3) AAbbCCDD
4) aabbCCDD
2 heterozygous loci/ 4 loci total = 50% heterozygosity
0 heterozygous loci/ 4 loci total = 0% heterozygosity
0 heterozygous loci/ 4 loci total = 0% heterozygosity
0 heterozygous loci/ 4 loci total = 0% heterozygosity
50%/4 = 12.5 mean heterozygosity
Measuring Genetic Variation in Natural Populations
Percent polymorphism = % of loci in the population that have at least two alleles.
Measure variation within the population as a whole.
1) AaBbCCDD
2) AABBCCDD
3) AAbbCCDD
4) aabbCCDD
Number of loci in the population = 4 – A, B, C, D
Number of loci that are polymorphic - 2 – A & B
2/4 = 50% polymoprphism
Mutation Rates
The mutation rate is a measure of the frequency of a given mutation per
generation (or per gamete, which is equivalent).
• Ordinarily, rates are given for specific loci.
• Thus the mutation rate for achondroplasia (short stature) is 6-13 mutants per
million gametes.
• This means that each gamete has ca. 1 chance in 100,000 of carrying a new
mutation for achondroplasia.
Mutation Rates