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Biased Substitutions in the
Human Genome:
Sex, Gambling and
Non-Darwinian Evolution
Tim Dreszer, Katie Pollard and David Haussler
Dreszer T. R., Wall G.D., Haussler D. and Pollard K.S.
Biased Substitutions in the Human
Genome:
The Footprints of Male-Driven
Biased Gene Conversion
Genome Res. 17:1420-1430 Epub: September 4, 2007. ISSN 1088-9051/07.
Where this Began:
Fastest Evolving Regions of the
Human Genome Show a
Surprising “Bias”
[1]
In Top 4 Regions:
AT pair replaced by GC or CG pair 33 times
GC replaced by AT pair only once
1
Pollard K.S., Salama S.R., King B., Kern A., Dreszer T., Katzman S., Siepel A., Pedersen J., Bejerano G.,
Baertsch R., Rosenbloom K.R., Kent J. and Haussler D. Forces Shaping the Fastest Evolving Regions in the
Human Genome. PLoS Genetics. 2(10):e168 Oct. 13, 2006.
Initial Terms
 AT pairs bond with 2 hydrogen bonds
and are here referred to as “Weak”
Pairs
 GC bond with 3 and are referred to as
“Strong” Pairs
 SNPs are single nucleotide
polymorphisms while “substitutions”
are single pair changes that have been
“fixed” in the genome.
 “Bias” here specifically refers to “Weak to Strong” SNPs or
substitutions.
This work finds surprising biased substitution patterns.
Large Scale Bias: Isochores
 In warm blooded vertebrate genomes, regions as
large as 300 kilobases dubbed “isochores” can be
strikingly higher or lower in GC content.[2]
 Isochores stretch across conserved and nonconserved sequences.
 The content of GC in genes is correlated with the
isochores they are within[3], and one study
suggests that the genes may lead the selection.[4]
2 Bernardi
G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. May 24, 1985. The mosaic
genome of warm-blooded vertebrates. Science. 228(4702):953-8.
3 Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. The mosaic genome of
warm-blooded vertebrates. Science. 228(4702):953-8. May 24, 1985.
4 Press W.H. and Robins H. Oct. 2006. Isochores Exhibit Evidence of Genes Interacting With the Large-Scale Genomic
Environment. Genetics, 174:1029-1040.
Three Possible Causes of Current
Human Bias and of Isochores
[5]
 Mutation Bias: variation in mutation rates in different
regions of the genome.[6]
 Natural Selection (fitness selection) for GC alleles
may have driven isochore formation[7], and may be
behind local GC content as well.
 Biased Gene Conversion (BGC) may result in a
pressure that pushes GC pairs to fixation at
recombination hot spots.[8]
5 Eyre-Walker A.
and Hurst L.D. July 2001. The evolution of isochores. Nat Rev Genet. 2(7):549-55.
N. April 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. 85(8):2653-7.
7 Bernardi G, Bernardi G. 1986. Compositional constraints and genome evolution. J. Mol Evol. 24(1-2):1-11.
8 Eyre-Walker A. June 22 1993. Recombination and mammalian genome evolution. Proc Biol Sci. 252(1335):237-43.
6 Sueoka
Biased Gene Conversion:
[9]
Mismatched SNP Repair in Heteroduplex During Recombination
T
GCTGTAGATCGTTG
CGACATCTAGCAAT
G
ACGTA
TGCAT
C
GATTACGTCGT
CTAATGCAGCA
A
Both mismatches are converted to “strong” G-C pairs, replacing “weak” SNPs.
9 Brown,
T. C., and J. Jiricny. 1988. Different base/base mispairs are corrected with different efficiencies and specificities in monkey
kidney cells. Cell 54:705–711.
Distinguishing between
the Three Models
 Mutation bias should result in similar patterns of
bias between SNPs and substitutions.[10]
 Natural Selection may result in a correlation
between biased substitutions and conservation.
 BGC may result in a correlation between biased
substitutions and current recombination hot spots
or rates.[11]
 BGC should be most easily recognized in clusters
of closely spaced substitutions. Clusters are not,
however, inconsistent with fitness selection.
10 Lercher
M.J., Urrutia A.O., Pavlícek A. and Hurst L.D. 2003. A unification of mosaic structures in the human genome. Hum. Mol.
Genetics, 12(19):2411-2415.
11 Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck,
B., Masson, G., Shlien, A., Palsson, S.T., Frigge, M.L., Thorgeirsson, T.E., Gulcher, J.R., and Stefansson, K. . 2002. A high-resolution
recombination map of the human genome, Nature Genetics, 31(3):241-247.
Mutation Bias?
SNPs in Humans (hg17)
3,424,895
Weak to Strong SNPs
1,368,922 ( 39.97 %)
Strong to Weak SNPs
1,506,024 ( 43.97 %)
Substitutions in Humans (hg17)
10,871,681
Weak to Strong
4,685,494 ( 43.10% )
Strong to Weak
4,650,554 ( 42.78% )
Bias by Window: G+C Content
Windows: Bias by Conservation?
Windows: Bias At Hotspots?
Bias Near Telomeres?
Bias by Substitution Density
Bias as a Social Disease: Zippers
Bias as a Social Disease: Heat
Biased Gang Members are Recruited
From Unbiased Individuals
SNPs:
Substitutions:
Mutation Bias is Rejected.
Assuming the rate of mutation and fixation
have not changed over the last 6my, biased
mutations are fixed in the genome in greater
proportion than they occur.
When examining clusters of biased
differences, the evidence is strikingly
against the biased mutation hypothesis.
Clusters are predicted by the BGC
hypothesis but are not contrary to a natural
selection model.
The Story is in the Data,
but How to Look At It?
Individual Weak to Strong Substitutions
don’t show the story well: too much noise.
Comparing windows of fixed size results in
comparing apples to oranges: a cluster of 3
with 2 WtoS compared to a cluster of 7 with
7 WtoS.
What is Needed: A measure of the degree to
which a single substitution is biased and
clustered.
With such a measure, mapping where this
phenomenon occurs might be revealing.
Geography of a Chromosome
UBCS or UC BS?
 Clusters are 5 or more substitutions within 300bp.
 Biased Clusters are at least 80% Weak to Strong substitutions.
 Biased Clustered Substitutions (BCS) are substitutions within biased
clusters.
 Expected BCS is the binomial probability of BCS within each 1mbp
bin.
Actual BCS
– Expected BCS
= Unexpected BCS
UBCS is
Unexpected
Biased
Clusters
Substitutions
Geography of a Chromosome Take 2
UBCS is Predictable
UBCS Rises Near the Telomeres of
All Human Autosomes
Chromosome 5 is Typical
Chromosome Y is an Exception
No Signal on Chromosome Y is
what would be expected if Biased
Gene Conversion is the Driving
force of UBCS.
 Recombination doesn’t occur on chromosome Y.
 Fitness Selection isn’t ruled out, but it doesn’t
predict a missing signal on Y.
Chromosome X is an Enigma
Is it Just that Sex is Mysterious?
The BGC model doesn’t predict a missing
signal on X: Chromosome X recombines so
there should be a signal.
Natural Selection doesn’t predict the
missing signal either. However, there may
be fitness based reasons for selecting GC
SNPs near the telomeres of autosomes that
do not apply to the sex chromosomes.
Is there a Clue in the PseudoAutosomal Regions?
Fun with Correlations
Conservative Bias?
Recruitment?
Recombination Hot Spots
Recombination Rate
Males are the Troublemakers!
Rank Troublemakers
History vs. Geography
BGC Model is Accepted
 While fitness selection cannot be ruled out, there is no
process known that would explain a fitness advantage of
increasing the GC content of mega-base regions by
selecting localized clusters of GC SNPs.
 Fitness selection cannot explain the correlation with
recombination rates or the lack of correlation with
conserved regions.
 Biased Gene Conversion explains all the observed data:
 Clusters of biased substitutions within 300 bases of each other.
 Selection of Biased Substitutions from Unbiased SNPs
 Correlation of UBCS with recombination rate.
 Lack of signal on the Y chromosome.
 Lack of signal on the X chromosome.
 Even the correlation of UBCS with GC content makes sense.
Why is this Striking?
These datasets are mutually exclusive! They represent a pattern in substitutions
occurring since humans and chimps diverged approximately 6mya.
UBCS Rises Near the Telomeres of
All Chimp Autosomes
UBCS Signal is Remarkably Similar
Between Human and Chimp Genomes
Stable BCS Accumulation is Revealing
 Moderate correlation between current recombination hotspots but
strong correlation with male recombination rates agrees with models
of hot spots moving[12,13] while regional recombination rates remain
steady.[14]
 The similarity of human and chimp UBCS profiles attests to a stable
force across 12 my of genetic divergence.
 The highly localized bias suggests an explanation for the origin of
isochores. The telomeres of autosomes may be Duret’s GC
factories[15], allowing the build up of isochores over millions of years.
 The borders between high and low GC regions seen today may
represent the historical record of chromosomal rearrangements.
12 Pineda-Krch
M. and Redfield R.J. April 2005. Persistence and Loss of Meiotic Recombination Hotspots. Genetics, 169:2319-2333.
W., Myers S.R., Richter D.J., Onofrio R.C., McDonald G.J., Bontrop R.E., McVean G.A.T., Gabriel S.B., Reich D.,
Donnelly P., Altshuler D. April 1, 2005. Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees. Science
308(5718):107-111.
14 Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. Oct. 14 2005. A fine-scale map of recombination rates and hotspots
across the human genome. Science. 310(5746):321-4.
15 Duret L., Eyre-Walker A. and Galtier N. Aug. 2006. A new perspective on isochore evolution. Gene 385:71–74.
13 Winckler
Chromosome 2 is an Exception
Current Recombination Rate is not
High in Zone of Fusion
Two Autosomes on a Date
Assuming:
1. The internal peak was created while the regions were still
telomeric.
2. Since fusion the region is no longer accumulating UBCS.
3. The force creating UBCS has been constant over the past
6my.
Then the fusion might be dated.
Using the ability to predict the UBCS signal at human telomeres
from the UBCS signal at chimpanzee telomeres, then the predicted
height minus the actual height of the chr2 peak may proportional to
the time that has elapsed since the fusion.
Estimated Fusion Date is 740,000 years ago with a CI95
of no more than 2.71 mya.
Chromosome 2 Fusion Dating
Non-Darwinian Selection
 BGC acts as a selection pressure[16], separate from
fitness. It selects GC SNPs over AT SNPs with enough
pressure that some of them are fixed into the genome.
 While the individual SNPs may have already been
tested as not too harmful, a newly selected cluster may
be a novel allele never before seen.
 If a single point mutation is far more likely to be
harmful than beneficial, what about a cluster of them?
 BGC selection can be expected to accelerate positive
selection.
 BGC selection can also be expected to compete with
and slow negative selection.
16
Nagylaki T. Oct. 1983. Evolution of a finite population under gene conversion. Proc. Natl. Acad. Sci. USA. 80(20):6278–6281.
Non-Darwinian Evolution Take 1
Despite a lack of correlation between UBCS and transcription density genome-wide, the
most extremely biased regions of the genome contain a disproportionate number of genes.
Non-Darwinian Evolution has
Sculpted Humans
Of the 10 top scoring regions of biased clustered
substitutions 4 are involved in brain development or
function! Eight of 10 are transcribed, while the other 2 are
predicted genes, transcribed in mammals.
Non-Darwinian Evolution Take 2
 Although there is no genome-wide SNP bias, some extremely
biased clusters of SNPs do exist.
 Two of the top five regions occur in genes associated with
cancer in humans (e.g., SERINC1[17] and CSMD1[18]).
 The region with the most biased SNPs (8 within 148 bp) falls in
the intron of a gene required for pain perception.[19]
 These data suggest that the force leading to the fixation of
clusters of biased changes is still active and may represent cases
where BGC is competing with purifying selection.
17 Zhang
M., Yu L., Wu Q., Zheng L.H., Wei Y.H., Wan B., Zhao S.Y. July 2003. Identification and characterization of TDE2, a
plasma-membrane protein with 11 transmembrane helices, and its variable expression in human lung cancer and liver cancer
tissues.
18 Scholnick S.B., Richter T.M. 2003. The role of CSMD1 in head and neck carcinogenesis.
Genes Chromosomes Cancer
38(3):281-283.
19 Kim E, Cho KO, Rothschild A, Sheng M. July 1996. Heteromultimerization and NMDA receptor-clustering activity of Chapsyn110, a member of the PSD-95 family of proteins. Neuron. 17(1):103-13.
Association of BGC with Male but not
Female Meiosis is Provocative
 It is well known that mutation rates are higher in males
than females[20, 21], which has been dubbed “male driven
evolution”.[22]
 While the higher mutation rate is attributed to the greater
number of cell divisions in male germ cells, this does not
explain the full increase.[23, 24, 25]
 It is not obvious why or how the dangers of BGC would
be tolerated in males while avoided in females.
20 Goetting-Minesky
MP, Makova KD. Sep. 4, 2006. Mammalian Male Mutation Bias: Impacts of Generation Time and Regional
Variation in Substitution Rates. J Mol Evol. [Epub ahead of print].
21 Crow JF. 1993. How much do we know about spontaneous human mutation rates? Environ. Mol. Mutagen. 21(4):389.
22 Li WH, Yi S, Makova K. Dec. 2002. Male-driven evolution. Curr. Opin. Genet. Dev. 12(6):650-6.
23 Lercher M.J., Williams E.J., Hurst L.D. Nov. 2001. Local similarity in evolutionary rates extends over whole chromosomes in
human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias. Mol
Biol Evol. 18(11):2032-9.
24 Filatov D.A., Charlesworth D. June 2002. Substitution rates in the X- and Y-linked genes of the plants, Silene latifolia and S.
dioica. Mol. Biol. Evol. 19(6):898-907.
25 Gaffney D.J., Keightley P.D. Aug. 2005. The scale of mutational variation in the murid genome. Genome Res. 15(8):1086-94.
Epub 2005 Jul 15.
“Wanna Get Lucky?”
A Male Reproductive Strategy?
 Females reproductive strategy treats every single gamete as
precious, since each has a high probability of becoming a child.
Females guarantee one good copy of the genome.
 Male gametes have an extremely low probability of success: there
are millions per mating.
 This allows a male strategy of rolling the dice in the form of
mutations and BGC.
 While most genetic changes are benign and some are harmful, one
in a million will be beneficial.
 “Sperm Selection”[26] or intra-mating sperm competition allows for
testing the gametes in order to select that one in a million. Thus
each mating is an evolutionary experiment!
 Warning: the sperm selection strategy requires that new mutations
are transcribed and tested.
26 Holt
W.V., Van Look K.J. May 2004. Concepts in sperm heterogeneity, sperm selection and sperm competition as biological
foundations for laboratory tests of semen quality. Reproduction. 127(5):527-35.
Transcription Associated Recombination
 It has been proposed that transcription-associated
recombination (TAR)[27, 28, 29, 30] might be driving BGC[31].
 If this were true, then the demands of gamete generation
would make BGC hard to avoid in males, while the
“maternal effect”[32] would explain how BGC is avoided in
females.
 Finally, sperm selection might mitigate some of the dangers
of new biased cluster alleles.
27 Aguilera A.,
2002. The connection between transcription and genomic instability. EMBO J. 21:195–201.
F., Piruat J.I. and Aguilera A. 1997. Recombination between DNA repeats in yeast hpr1Delta cells is linked to transcription
elongation. The EMBO Journal 16:2826–2835.
29 Bell S.J, Chow,Y.C., Ho,J.Y. and Forsdyke,D.R. 1998. Correlation of chi orientation with transcription indicates a fundamental
relationship between recombination and transcription. Gene, 216:285–292.
30 Nickoloff J.A. and Reynolds R.J. 1990. Transcription stimulates homologous recombination in mammalian cells. Mol. Cell. Biol.
10:4837–4845.
31 Vinogradov A.E. Sept. 1, 2003. Isochores and tissue-specificity. Nucleic Acids Res. 31(17):5212–5220.
32 Dobzhansky T. Maternal Effect as a Cause of the Difference between the Reciprocal Crosses in Drosophila Pseudoöbscura. Proc
Natl Acad Sci U S A. 1935 Jul;21(7):443-6.
28 Prado
Loose Ends
 The TAR model explains the finding that the most biased
regions are disproportionately transcribed.
 If sub-telomeric regions are GC factories building
isochores, then the TAR model explains why
Genes appear to lead the accumulation of GC in GC
rich isochores.[33]
Widely expressed housekeeping genes are more often
found in GC rich isochores than are tissue specific
genes.[34]
33 Press
W.H. and Robins H. Oct. 2006. Isochores Exhibit Evidence of Genes Interacting With the Large-Scale Genomic
Environment. Genetics, 174:1029-1040.
34 Vinogradov A.E. Sept. 1, 2003. Isochores and tissue-specificity. Nucleic Acids Res. 31(17):5212–5220.
Sex, Gambling and
Non-Darwinian Evolution
 BCS are the Footprints of Male Driven BGC.
 BGC is a Non-Darwinian selective pressure that leads
to faster evolution but also can slow purifying
selection.
 Female reproductive strategy goes to extra effort to
ensure the genome is protected.
 Male reproductive strategy makes each gamete a roll of
the dice, while each mating is an evolutionary
experiment.
 BGC is a stable force that has sculpted human and
chimpanzee evolution.
To Do:
• Other Species? How widespread?
Primates, Placental Mammals?
Marsupials? Birds?
• Neanderthals and Chr2?
• Duret’s challenge?
• What is going on in PAR?
• Wet lab work to tie down TAR -> BGC.
To See:
http://www.soe.ucsc.edu/research/compbio/ubcs/
Thanks
 David Haussler for taking me into his lab and putting me to work
on something so interesting.
 Katie Pollard for patiently explaining to me all the things I should
already have known, and putting up with my limitations.
 The Genome Browser and all contributors.
 Clint, some lab macaque and Watson and Crick
 Greg Wall for statistical work.
 Daryl Thomas for generating some of the datasets.
 Laurent Duret for excellent feedback.
 Bill Press for taking an interest.
 My wife for supporting me throughout, my son for being my
sounding board and my daughter for preventing me from
finishing before the best discoveries were made.