Download lecture 01 - sources of variation - Cal State LA

Biol 418: Advanced Evolution
Course website:
instructional1.calstatela.edu/pkrug
NO WWW at beginning!
click on “Bio 418” to get powerpoint files, study guides, syllabus
Pre-requisite: Evolution (Biol 350)
- undergraduate students without this pre-req will be
dropped without notice
Course Overview – BIOL 418
Co-taught by Drs. Krug and Ellingson
[email protected]
[email protected]
one midterm exam
one final exam
four in-class exercises done (a) at home, then
(b) in small groups during class, based on
reading the primary scientific literature
Evolution: genetic change over time
Things to review/remember:
- populations evolve; individuals do not
- all evolution does not produce adaptation
- much evolution results from genetic drift (random change)
- change can be mal-adaptive (bad)
- the raw material of evolution is genetic variation present
in a population
- without underlying variation, a population may not be
capable of evolving
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
1) What alleles are present (variants of a given gene)?
2) How are those alleles arranged into genotypes?
3) How do (i) allele combinations, and (ii) rearing environment
together result in the phenotype?
 The distribution of alleles, genotypes and phenotypes in
a population are then acted on by (i) genetic drift, and
(ii) various forms of selection, resulting in evolution
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
AA
Aa
aa
aa Aa AA
- this population is
polymorphic at this
genetic locus
(= has more than one allele)
allele frequencies can change
AA
AA
AA
AA
AA
AA
- this population is fixed for
the “A” allele at this locus
no evolution is possible
at this locus until new
alleles enter population
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Aa
Aa
Aa
aa Aa AA
Aa Aa
AA AA
AA
aa
aa
aa aa
AA
3 different populations with same allele frequencies:
A = a = 0.5
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
At HW equilibrium, genotype frequencies
can be calculated from allele frequencies
p = frequency of A allele = 8/16 = 0.5
q = frequency of a allele = 8/16 = 0.5
Hardy-Weinberg
equilibrium
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
At HW equilibrium, genotype frequencies
can be calculated from allele frequencies
p2 + 2pq + q2 = 1
(0.5)2 + 2(0.5)(0.5) + (0.5)2 = 1
Hardy-Weinberg
equilibrium
0.25 + 0.5 + 0.25 = 1
AA
Aa
aa
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Aa
Aa
Aa
aa Aa AA
Aa Aa
What is unusual in this population?
What could have caused it?
AA AA
AA
aa
aa
aa aa
AA
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Aa
Aa
Aa
aa Aa AA
Aa Aa
AA AA
AA
aa
aa
aa aa
AA
What is unusual in this population? - too many heterozygotes
What could have caused it?
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Aa
Aa
Aa
aa Aa AA
Aa Aa
AA AA
AA
aa
aa
aa aa
AA
What is unusual in this population? - too many heterozygotes
What could have caused it? - overdominance (selection)
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Aa
Aa
Aa
aa Aa AA
Aa Aa
What is unusual in this population?
What could have caused it?
AA AA
AA
aa
aa
aa aa
AA
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Aa
Aa
Aa
aa Aa AA
Aa Aa
AA AA
AA
aa
aa
aa aa
AA
What is unusual in this population? - too many homozygotes
What could have caused it?
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
- what alleles are present (variants of a given gene)?
- how are those alleles arranged into genotypes?
AA
Aa
Aa
aa Aa aa
Aa AA
Aa
Aa
Aa
aa Aa AA
Aa Aa
AA AA
AA
aa
aa
aa aa
AA
What is unusual in this population? - too many homozygotes
What could have caused it? - inbreeding, underdominance,
migration
Evolution: genetic change over time
The raw material of evolution is genetic variation, including:
1) What alleles are present (variants of a given gene)?
2) How are those alleles arranged into genotypes?
3) How do (i) allele combinations, and (ii) the environment,
together result in the phenotype?
- Is a trait highly heritable, or mostly due to environment?
- How many loci contribute to a given trait – 3, 300, 3000?
- Is a trait phenotypically plastic? (adjustable on the fly)
Sources of genetic variation
What are the sources of genetic variation in natural populations?
1) mutation
2) gene flow (dispersal between populations)
3) sexual reproduction
4) hybridization with related species
Sources of genetic variation 1: mutation
Mutation is the ultimate source of new genetic variation
Mutation rate = rate at which changes in the DNA actually occur
Substitution rate = rate at which changes appear and persist
long enough for us to measure them, by sequencing DNA
from multiple individuals in a population
Subtle but important distinction: Many, perhaps most, mutations
are bad for your fitness (or even lethal). These mutations tend
to get you killed, or to kill you. We won’t “see” these mutations
when we sequence DNA from a bunch of individuals, because
those really bad mutants are already dead.
Substitution rate is what we can easily measure; it is much lower
than the actual mutation rate.
Two kinds of DNA substitutions
Transition mutations are observed more frequently, because
they are not fixed as often by DNA repair enzymes
 that is, they escape correction so we see them more often
Sources of genetic variation 1: mutation
Some mutations are harder for DNA repair enzymes to detect,
so escape correction and thus occur more often
Transitions: A
G, C
T
- replace a purine w/ a purine
or pyrimidine w/ pyrimidine
This class of mutations is observed more frequently, because
they are not fixed as often by DNA repair enzymes
Transversion: everything else; more rare
Sources of genetic variation 1: mutation
Transversions are usually caught & corrected by DNA repair
enzymes, so get detected less often in sequence data
inserted
guanine
Transversions stick two
non-complimentary bases
up against each other
 disrupts DNA helix,
making bulge
 more likely to get noticed
& fixed by repair enzymes
Sources of variation 1: mutation
1) transitions are more common than transversions
2) substitutions that (i) occur in non-coding regions of DNA, or
(ii) result in synonymous amino acid substitutions, are
more likely to persist in natural populations
 because most changes to the amino acid sequence of any
protein are likely to make the protein worse, not better, they
are typically removed by selection before we can see them
 thus, the substitution rate is lower than the actual mutation
rate; many mutations disappear before we have a chance
to measure them
Sources of variation 1: mutation
1) transitions are more common than transversions
2) substitutions that (i) occur in non-coding regions of DNA, or
(ii) result in synonymous amino acid substitutions, are
more likely to persist in natural populations
i) mutations in non-coding DNA do not usually affect the
phenotype, so are termed ‘silent’
ii) synonymous substitutions change one codon to another
for the same amino acid, thus do not change the protein
- usually occur at the 3rd codon position, sometimes 1st
Sources of variation 1: mutation
Sources of variation 1: mutation
1) transitions are more common than transversions
2) substitutions that (i) occur in non-coding regions of DNA, or
(ii) result in synonymous amino acid substitutions, are
more likely to persist in natural populations
i) mutations in non-coding DNA do not usually affect the
phenotype, so are termed ‘silent’
ii) synonymous substitutions change one codon to another
for the same amino acid, thus do not change the protein
iii) non-synonymous substitutions change the amino acid at
a given position, thus changing the protein and potentially
the phenotype
Sources of variation 1: mutation
non-synonymous substitutions tend to be less commonly
observed than synonymous substitutions, but that doesn’t
mean they occur less often
 in fact, they must occur more often; why?
 if they occur more often, why are non-synonymous mutations
only rarely observed in DNA sequences?
DNA sequence alignment
E_sp19
Edio_2
Edio_4
Edio_3
Edio_1
04Pan01
04Pan04
04Pan05
04Pan07
04Pan09
04Pan10
04Pan16
06Jam01
06Jam02
06Jam09
06Jam12
06Dom02
06Dom03
06Dom04
06Dom05
06Dom10
07Gei01
07Gei02
07Gei03
07Gei05
07Gei08
07Swe01
07Swe02
07Swe04
07Swe09
07Swe10
07LSS01
07LSS02
07LSS04
10NEx01
10NEx02
10NEx03
10NEx05
TGGTCTAGTCGGAACTGGTTTAAGATTATTAATTCGATTTGAATTAGGAACTTCTGGTGCTTTCCTGGGTGATGATCATTTCTACAATGTTATTGTTAC
...CT....A..G..C..A.....G..................C....T..............TT.A..............T..T.....C........
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.T...........C........G...........C..TT.A........C..C.....T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.T...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.T..............GC....G...........C..TT.A........C.....T..T..............
....T.......T............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T....T..G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......T............C.CC.......G...........G........C.....TT.A........C..C..T..T..............
...CT.......T............C.CC................G..G...........C..TT.A........C..C.....T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
DNA sequence alignment
E_sp19
Edio_2
Edio_4
Edio_3
Edio_1
04Pan01
04Pan04
04Pan05
04Pan07
04Pan09
04Pan10
04Pan16
06Jam01
06Jam02
06Jam09
06Jam12
06Dom02
06Dom03
06Dom04
06Dom05
06Dom10
07Gei01
07Gei02
07Gei03
07Gei05
07Gei08
07Swe01
07Swe02
07Swe04
07Swe09
07Swe10
07LSS01
07LSS02
07LSS04
10NEx01
10NEx02
10NEx03
10NEx05
TGGTCTAGTCGGAACTGGTTTAAGATTATTAATTCGATTTGAATTAGGAACTTCTGGTGCTTTCCTGGGTGATGATCATTTCTACAATGTTATTGTTAC
...CT....A..G..C..A.....G..................C....T..............TT.A..............T..T.....C........
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.T...........C........G...........C..TT.A........C..C.....T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.T...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.T..............GC....G...........C..TT.A........C.....T..T..............
....T.......T............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T....T..G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......T............C.CC.......G...........G........C.....TT.A........C..C..T..T..............
...CT.......T............C.CC................G..G...........C..TT.A........C..C.....T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
1) Most observed substitutions in real data
are transitions (A G, C T)
2) changes at 3rd codon position > 1st >> 2nd
Sources of variation 1: mutation
1) transitions are more common than transversions
2) synonymous substitutions are more common than
non-synonymous changes when comparing sequences of
individuals in natural populations (for most loci)
3) non-synonymous substitutions resulting in conservative
amino acid changes are more likely to survive
- conservative = swapping one residue for another of the
same size, charge, and/or polarity
- for the same reasons as discussed previously, such
changes are less likely to drastically alter protein function,
and so are less likely to be removed promptly by selection
Sources of variation 1: mutation
3) conservative amino acid changes are more likely to survive
- swapping non-polar for another non-polar amino acid
- swapping a polar for another polar residue
DNA sequence alignment
E_sp19
Edio_2
Edio_4
Edio_3
Edio_1
04Pan01
04Pan04
04Pan05
04Pan07
04Pan09
04Pan10
04Pan16
06Jam01
06Jam02
06Jam09
06Jam12
06Dom02
06Dom03
06Dom04
06Dom05
06Dom10
07Gei01
07Gei02
07Gei03
07Gei05
07Gei08
07Swe01
07Swe02
07Swe04
07Swe09
07Swe10
07LSS01
07LSS02
07LSS04
10NEx01
10NEx02
10NEx03
10NEx05
TGGTCTAGTCGGAACTGGTTTAAGATTATTAATTCGATTTGAATTAGGAACTTCTGGTGCTTTCCTGGGTGATGATCATTTCTACAATGTTATTGTTAC
...CT....A..G..C..A.....G..................C....T..............TT.A..............T..T.....C........
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T....A..G..C..A.....G...C..............C.T..T..............TT.A..............T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C........T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.T...........C........G...........C..TT.A........C..C.....T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T....T..G............C.C....................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.T...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.T..............GC....G...........C..TT.A........C.....T..T..............
....T.......T............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......G............C.TC...................G...........C..TT.A.....C..C..C..T..T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T....T..G............C.C...............C....G...........C..TT.A........C.....T..T..............
....T.......T............C.CC.......G...........G........C.....TT.A........C..C..T..T..............
...CT.......T............C.CC................G..G...........C..TT.A........C..C.....T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......G............C.C...............C....G...........C..TT.A........C..C..T..T..............
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
....T.......T............C.TC...................G...........C..TT.A........C..C..T..T...........C..
Amino acid alignment
E_sp19
Edio_2
Edio_4
Edio_3
Edio_1
04Pan01
04Pan04
04Pan05
04Pan07
04Pan09
04Pan10
04Pan16
06Jam01
06Jam02
06Jam09
06Jam12
06Dom02
06Dom03
06Dom04
06Dom05
06Dom10
07Gei01
07Gei02
07Gei03
07Gei05
07Gei08
07Swe01
07Swe02
07Swe04
07Swe09
07Swe10
07LSS01
07LSS02
07LSS04
10NEx01
10NEx02
10NEx03
10NEx05
10NPr01
GLVGTGLSLLIRFELGTSGAFLGDDHFYNVIVTAHAFVMIFFMVMPLMIGGFGNWMVPILIGAPDMSFPRMNNMSFWLLPPSFIFLLSSSLVEGGAGTG
...................................................................................................
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Amino acid alignment
E_sp19
Edio_2
Edio_4
Edio_3
Edio_1
04Pan01
04Pan04
04Pan05
04Pan07
04Pan09
04Pan10
04Pan16
06Jam01
06Jam02
06Jam09
06Jam12
06Dom02
06Dom03
06Dom04
06Dom05
06Dom10
07Gei01
07Gei02
07Gei03
07Gei05
07Gei08
07Swe01
07Swe02
07Swe04
07Swe09
07Swe10
07LSS01
07LSS02
07LSS04
10NEx01
10NEx02
10NEx03
10NEx05
10NPr01
GLVGTGLSLLIRFELGTSGAFLGDDHFYNVIVTAHAFVMIFFMVMPLMIGGFGNWMVPILIGAPDMSFPRMNNMSFWLLPPSFIFLLSSSLVEGGAGTG
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one S  N change
serine (-OH) to
glutamine (-CONH2)
Sources of variation 1: mutation
1) transitions are more common than transversions
2) synonymous substitutions are more common than
non-synonymous changes when comparing sequences of
individuals in natural populations (for most loci)
3) conservative amino acid changes are more likely to survive
4) different positions on a protein evolve at very different rates
- surface may evolve more easily than core
- sites involved with catalysis, or contacting partner proteins
Some genes are more toleratant of substitutions (many changes
have little effect on protein structure/function); other genes
show fewer substitutions (amino acid change is usually harmful)
Mutation rates also vary among chromosomes, and between
chromosome regions, creating “local rates” of mutation
- variation in chromatin structure affects local rates
Prendergast et al. 2007
- reporter genes inserted in different places throughout the
genome in human cell lines had 60-fold difference in
mutation rate, depending on where it was inserted
Lichtenauer-Kaligis et al. 1993
Whitkopp & Kilay 2011,
Nat. Rev. Gen.
mutation rate
(per DNA site per generation)
10-9 low
ribosomal
rRNA
conservative
replicators
high 10-8
genes
individuals
immune
receptors
mutator
strains
species
C. elegans
C. briggsae
[cited rates are for animals; for bacteria, rates are 10x higher]
Mutation rates are higher for DNA passed through males than
through females, as predicted by Haldane in 1947
- more cycles of cell division are involved in spermatogenesis,
allowing for more errors in DNA replication per generation
- generally confirmed by genetic studies:
- ‘male-driven evolution’ or male-biased substitution rates
are ~5-fold higher for male primates
Makova & Li 2002, Nature
- not a function of the Y-chromosome; male mutation rate
~5x higher than female’s rate in birds, yet female birds
are the heterogametic sex (WZ, vs. WW for male birds)
Ellegren & Fridolfsson 1997, Nature Genet.
In 2011, the 1st whole-genome sequencing comparison of two
human familes (two parents, one child) found:
- 49 and 35 germline de novo mutations (in kid, not parents)
“germline” = in sperm/eggs; will be passed to offspring
- 1,586 non-germline mutations (somatic origin; non-heritable)
- in one family, 92% of germline mutations were from paternal
germline
- in 2nd family, 64% of germline mutations were from maternal
germline
Conrad et al. 2011, Nat. Gen.
 high variation in mutation rates between human families
human genome size: 3 x 109 per gamete
Mutation as a cost of sexuality
Given all these constraints on evolution, why do proteins ever
evolve at all..?
Mutation is generally understood as an evolutionary
consequence of costs of DNA proof-reading and repair,
especially for sexually-reproducing organisms
- meiosis allows sex, which creates new allele combinations,
but appears to be very hard to achieve without a certain
level of error (mistakes in copying DNA = mutation)
- we could mutate less, but at too high of a cost to be
favored by selection
Mutation via hitch-hiking in asexuals
In asexual or clonally reproducing organisms (e.g., bacteria)
mutator alleles can become linked to rare, beneficial mutations
that they create, and thus “hitch-hike” to high frequency
DNA proofreading gene
wt = wild-type
(normal)
mutation creates a sloppy allele
of proof-reading enzyme..“mutator”
wt wt
M wt
other genes
affecting fitness
wt wt wt
1) “Mutator” allele arises randomly; creates a strain that
mutates at a higher frequency
Mutation via hitch-hiking in asexuals
1) “Mutator” allele arises randomly, creates a high-mutation strain
2) Most mutations will lower fitness, and be lost...
wt wt
M wt
M wt
M wt
wt wt wt
wt wt
wt = wild-type
(normal)
= deleterious
(bad) mutation
wt
M
wt wt
wt
Mutation via hitch-hiking in asexuals
1) “Mutator” allele arises randomly, creates a high-mutation strain
2) Most mutations will lower fitness, and be lost...
wt wt
M wt
M wt
M wt
wt wt wt
wt wt
wt
M
wt wt
wt
Mutation via hitch-hiking in asexuals
1) “Mutator” allele arises randomly, creates a high-mutation strain
2) Most mutations will lower fitness, and be lost...
wt wt
M wt
wt wt
wt wt wt
wt wt wt
wt wt
wt wt
wt wt
wt wt wt
wt wt wt
wt wt wt
wt wt
wt wt wt
wt wt wt
wild-type would appear to win,
and out-reproduce Mutator strain
Mutation via hitch-hiking in asexuals
1) “Mutator” allele arises randomly, creates a high-mutation strain
2) Most mutations will lower fitness, and be lost...
wt wt
new allele that
doubles fitness
M wt
wt wt wt
M
3) However, beneficial mutations
(normally rare) will occur more
wt wt wt
often by chance in Mutator strains..
4) Now, Mutator allele of DNA proof-reading enzyme is linked
to the beneficial allele it created through ‘sloppy work’
Mutation via hitch-hiking in asexuals
1) “Mutator” allele arises randomly, creates a high-mutation strain
2) Most mutations will lower fitness, and be lost
3) However, beneficial mutations (normally rare) will occur more
often by chance in Mutator strains
4) Now, Mutator allele of DNA proof-reading enzyme is linked
to the beneficial allele it created through ‘sloppy work’
5) Wildtype proof-readers get out-competed due to lower fitness
M
M
M
M
wt wt
wt wt wt
wt wt
wt wt wt
M
wt wt wt
M
wt wt wt
wt wt wt M
wt wt wt
wt wt wt
Mutation via hitch-hiking in asexuals
1) “Mutator” allele arises randomly, creates a high-mutation strain
2) Most mutations will lower fitness, and be lost
3) However, beneficial mutations (normally rare) will occur more
often by chance in Mutator strains
4) Now, Mutator allele of DNA proof-reading enzyme is linked
to the beneficial allele it created through ‘sloppy work’
5) Wildtype proof-readers get out-competed due to lower fitness
6) This phenomenon – “genetic hitch-hiking” – occurs easily in
clonal species because recombination (sex) rarely separates
the mutator alleles, and the beneficial alleles
with which they become associated
M
(by chance) on the chromosome
wt wt wt
For most of the last century, it was assumed that differences
between species were due to different, species-specific
proteins that each had evolved
 since the genomic revolution, it has become clear that
instead, many evolutionarily important mutations affect
not the protein product itself, but gene expression
- how much is a gene expressed?
- in what tissues?
- when during development?
Whitkopp & Kilay 2011,
Nat. Rev. Gen.
Mutations affecting any of these can produce dramatic
changes in phenotype, behavior, and life history
Such mutational changes affect enhancers and promoters,
non-coding DNA that controls gene expression
A given gene may be under the control of multiple enhancers,
each one switching that gene on in a subset of tissues, or
at different times in development
- mutations in an enhancer can alter the timing or expression
pattern of a gene in one tissue type without affecting the
expression at other times or in other tissues, which will be
controlled by other enhancers
- this restricts the effects of a mutation to one tissue or stage,
whereas a change in the protein itself will affect all cells
all else being equal, a mutation in an enhancer is less
likely to kill you than a mutation in the gene that enhancer
controls (modularity)
promoters and enhancers regulate gene expression (a) in a
tissue-specific manner, that (b) can vary during development
A given gene may be under the control of multiple enhancers,
each one switching that gene on in a subset of tissues, or
at different times in development
early development, leg buds
mid-development, antennae
late development, wing buds
late development, tail
four enhancers direct tissue-specific
and timing-dependent expression of
a key gene (turn on gene where colored)
Consider a gene that triggers cell growth early in development
of body appendages; 4 different tissue-specific enhancers
turn this gene on at different times, in different places
A mutation in the protein ITSELF, causing let’s say, too much
cell growth... causes too much cell growth EVERYWHERE
Happy normal bug
Horrible freak monster; dies
A mutation in one enhancer can cause substantial changes in
phenotype without disrupting the rest of normal development
Happy normal bug
Few extra legs (possibly beneficial);
otherwise normal
 “modularity” means restricted change
 these kinds of cis-regulatory mutations are now known to
explain the bulk of phenotypic differences between species
Mutations in the enhancer HACNS1 led to a novel activity in
human evolution
 this enhancer now activates genes in the developing limbs
of humans, but does not have this activity in our closest
relatives
Prabhakar et al.
2008,Science
Loss of enhancers can lead to significant evolutionary change
- 509 regions containing possible enhancers are highly
conserved between chimps and other mammals, but
are missing from humans
- these deletions are associated with some loss of function
(sensory organs, penile spines) and gain of other function
(expanded brain capacity)
McLean et al. 2011, Nature
Transposons (“jumping genes”) can move enhancers into
novel locations, creating rapid evolutionary change
All these kinds of non-traditional mutations can produce
dramatic changes in phenotype, behavior, and life history
Another evolutionarily important type of mutation involves sites
that regulate alternative splicing of proteins
Barbosa-Morais et al. 2012, Science
exon 1
exon 2
intron
mRNA splicing
exon 3
intron
unspliced
mRNA
(removes intron sequences)
spliced
mRNA
encodes full-length
version of protein
goes to ribosome
Another evolutionarily important type of mutation involves sites
that regulate alternative splicing of proteins
Barbosa-Morais et al. 2012, Science
exon 1
exon 2
intron
exon 3
intron
unspliced
mRNA
mutations can occur at the intron-exon
border that cause a different pattern of
splicing in some tissues, leaving that
exon out of the final mRNA message
Another evolutionarily important type of mutation involves sites
that regulate alternative splicing of proteins
Barbosa-Morais et al. 2012, Science
exon 1
exon 2
intron
exon 3
intron
unspliced
mRNA
alternative
splicing
encodes full-length
version of protein
encodes shorter
version of protein with
modified function
Another evolutionarily important type of mutation involves sites
that regulate alternative splicing of proteins
- primates have more
alternative splicing
sites (AS) in their
genes than other
vertebrates
- frequency of AS
increased sharply
during the evolution
of humans in brain
and testes tissues,
compared with other
primates
Barbosa-Morais et al. 2012, Science