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Primate Comparative Genomics
“…man’s position in the animate world is an indispensable preliminary to the proper understanding of his relations to the universe – and this again resolves itself, in the long run, into an inquiry into the nature and the closeness of the ties which connect him with those singular creatures (the Great Apes) whose history has been sketched in the preceding pages.”
-Thomas H. Huxley-Man’s Place in Nature, 1894
Humans and Chimps
Homo sapiens à 99.9% identicalHomo sapiens and Pan troglodytes à 99.0% identical
Why sequence chimps?
Two white papers.http://www.genome.gov/11008056
Chimps Are Resistant To Many Human Diseases
Comparison of disease susceptibility between chimps and humans
Condition Human Chimp
HIV progression to AIDS common very rareInfluenza A symptoms moderate/severe mildHepatitus B/C complications moderate/severe mildPlasmodium falciparum malaria susceptible resistantMenopause universal rareE. Coli K99 gastroenteritis resistant sensitiveAlzheimer’s disease pathology complete incompleteEpithelial cancers common rareSource: Olson, M.V. et al. White paper advocating the complete sequencing of the common chimpanzee, Pan troglyodytes, (2002)
Chimp sequence can inform our unique population history
Kasserman et al (2001) Nat. Genet. 27: 155-56
Chimps can inform our unique population history
• Fixation of deleterious alleles during bottlenecks
• Chimp genome might offer a “fix” to common diseases
speech+speech--
hypertension+
hypertension--
obesity+obesity-- bipedal+
bipedal--
speech+
hypertension+obesity+
bipedal+
Chimp sequence can help detect selection
• Important to know the ancestral allele• Over-representation of the non-ancestral allele can
suggest selection
A
AA
AB B
BB
BBBBBB
BB
B
AB
B
BB
A allele fixed in Chimps
A and B are polymorphic in Humans
Only species appropriate for comparison of fast moving regions
• Pericentric duplications• Subtelomeric repeats• Y-chromosome• 5-7% of the genome is in large segmental
duplications
What does the genome tell us?
• (Roughly) same size genome (3.1 GB)• (Roughly) same number of genes (~20,500)• (Roughly) same genes• Large number of papers reporting specific
differences between human and chimps• Many papers also claim to detect positive selection
on specific human genes
Not too much yet…
Let’s do the math
How many differences do we need to look at?(3 x 109 bp) (1% divergence) (50% in humans) = 15 million bp
In coding DNA?(15 million bp) (1.5% coding) (75% non-synonomyous) =169,000 bpor about 7 non-synonomyous changes per gene
Non-coding DNA?(15 million bp) (3.5% under selection) = 525,000 bp
What are the possibilities?
• Gene loss• Gene gain• Gene mutation (a few or many)• Gene regulation• Something else?
Inter- versus Intraspecific Variation
He (man) resembles them (apes) as they resemble one another – he differs from them as they differ from one another.
-Thomas Huxley-Man’s Place in Nature, 1894
Gene Loss
Hypothesis: Humans have lost (one or more) genes compared to chimps, and it is the loss of those functions that accounts for our “humanness”
Sialic Acid Biologyan example of database mining
Chou et al. (1998) Proc. Natl. Acad. Sci. USA 95, 11751-11756
• Apes have lots of Neu5Gc, humans very little• Neu5Gc is located on the surface of epithelial cells• Neu5Gc is present in very low levels in the brain even
in animals that have lots of Neu5Gc
hydroxylase
humanchimpgorillamouse
A 92 bp deletion in the CMP-Neu5a hydroxylase is specific to the human lineage
ATGATGATGATG
Indels are ~50% of human-chimp differencesFrazer et al (2003) Genome. Res. 13: 341-346Locke et al. (2003) Genome. Res. 13: 347-357
Gene Gain
Hypothesis: Humans have gained (one or more) genes compared to chimps, and it is the gain of these new functions that accounts for our “humanness.”
Morpheus Gene Family
Johnson et al. (2001) Nature 413:514-519
Morpheus Gene family
Johnson et al. (2001) Nature 413:514-519
• 20 Kb duplicated segment on short arm of chromosome 16
• 98% identity in introns/non-coding DNA, 81% identity in exonic DNA
• Ka/Ks tests indicate (possibility of) extreme positive selection
• Gene family has no homology to known genes
Morpheus Gene Family
Gene Mutation
Hypothesis: Humans acquired (one or more) substitutions in the coding regions of their genes that alter the functions of those proteins so as to account for our “humanness.”
What about organism specific substitutions?
http://sayer.lab.nig.ac.jp/~silver/
C-C chemokine receptor (nucleotides 1 to 60)Human_1 ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGC Human_2 ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGC Human_3 ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGC Human_4 ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGC Chimp_1 ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCGATTATTATACATCGGAGCCCTGC Chimp_2 ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCGATTATTATACATCGGAGCCCTGC Chimp_3 ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCGATTATTATACATCGGAGCCCTGC Goril_1 ATGGATTATCAAGTGTCAAGTCCAACCTATGACATCGATTATTATACATCGGAGCCCTGC Goril_2 ATGGATTATCAAGTGTCAAGTCCAACCTATGACATCGATTATTATACATCGGAGCCCTGC Goril_3 ATGGATTATCAAGTGTCAAGTCCAACCTATGACATCGATTATTATACATCGGAGCCCTGC
************************* ********** ***********************
Problem: How can we make a conclusion based on one substitution?
Detecting Selective Sweeps• Selective sweeps are (thought to be) accompanied
by a local reduction in diversity• Test for overabundance of low frequency alleles
(Tajima’s D)
Apadted from Carroll, S. (2003) Nature 422:849-57
beneficial mutation arises Selection drives mutation to fixation mutation/recombination
FOXP2, The Human Speech Gene?1) Mapped in families with inherited speech
defects (normal IQ)2) Forkhead transcription factor
FOXP2 Nucleotide Substitutions
Enard et al. (2002) Nature 418, 869-72
FOXP2, The Human Speech Gene?
Enard et al. (2002) Nature 418, 869-72
• Sequencing of adjacent non-coding DNA revealed an excess in the number of low frequency alleles relative to what would be expected given neutral DNA in a randomly mating population of constant size
• Tajima’s D = -2.20 (P<0.01)
Gene Expression
Hypothesis: It is not the structural differences in proteins, but rather their differences in expression between humans and chimps that account for our “humanness.”
Differences in Gene Expression in the Brain?Enard et al (2002) Science 296, 340-343.
microarrays
2D Gels
Neutral Theory of Gene Expression?
• Consider how one might construct a neutral theory of gene expression akin to the neutral theory of gene mutation
1) What is the sequence of the normal Human Genome?
2) What accounts for the genetic differences between individuals?
Finding Segmental Duplications in the Human Genome
Bailey et al (2002) Science 297:1003-07
Segmental Duplications in the Human Genome
Bailey et al (2002) Science 297:1003-07
Polymorphism in Segmental Duplications
Iafrate et al (2004) Nat Genet 36:949-51
Polymorphism in Segmental Duplications
• CGH studies find many copy number polymorphisms in segmental duplications (~12 per individual)
• Rare and common polymorphisms• Many overlap coding regions• Critical for the interpretation of
amplifications in cancers• Responsible for phenotypic differences
between people?
SNPs/Hap Map/1000 GenomesThe International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain
Questions
1. How many sub-populations best partition the data?
2. How strong is the evidence for the clusters?3. Do the inferred clusters correspond to our
notions of race, ethnicity, ancestry, or geography?
4. Given the inferred clusters can we accurately can we classify new individuals?
5. Can we identify population admixture or migration events?
Attempts to group humans by genotype
p and Fst
1. p, average nucleotide diversity (~1 in 1000 bp)
2. Fst, proportion of genetic variation that can be ascribed to differences between populations (~10%)
Summary of Findings• p and Fst are small• Diversity within “African” populations is
highest• Unsupervised clustering tends to support
either 3 or 4 sub-populations depending on number and type of markers and individuals included in the study, but the composition of the groups are often different in different studies
A contradiction?
• Although they differed on the extent and composition of sub-populations, so far all studies have found evidence of significant sub-structure in human populations
• And yet, all studies agree that Fst is small (between 3-15%)
See review by Jorde and Wooding (2004) Nature Genet. 36: S28-S33
Small Fst does not imply lack of structure
A1
D2
B2
A1
B2
A1
A1
A1A2
A2D2
A1C1
C2
A1
B1
B1
B1A1
C1A2D1A2
A1C2
A1D2
C2
D1D1
A1
C1
D1
B2E2
E2
E1E1E1E1
E2
E2
E2
C2
Clustering human populations by genotype
K-means clustering of gene expression data
• Pick a number (k) of cluster centers
• Assign every gene to its nearest cluster center
• Move each cluster center to the mean of its assigned genes
• Repeat 2-3 until convergence
EM-based clustering of genotype data
• Pick a number (k) of sub-populations
• Assign every individual to a sub-population based on the allele frequencies in the sub-population
• Recalculate the allele frequencies in each sub population
• Repeat 2-3 until convergence
An ExampleI1= (A1,B1,C2)I2= (A1,B1,C2)I3= (A1,B2,C2)I4= (A2,B2,C1)I5= (A1,B1,C1)I6= (A1,B1,C2)I7= (A1,B1,C2)I8= (A2,B2,C2)I9= (A1,B2,C1)I10= (A2,B1,C2)I11= (A2,B2,C2)I12= (A2,B2,C2)
12 individuals genotyped at three different independent biallelic loci
k1 k3k2
I1= (A1,B1,C2)I2= (A1,B1,C2)I3= (A1,B2,C2)I4= (A2,B2,C1)
I5= (A1,B1,C1)I6= (A1,B1,C2)I7= (A1,B1,C2)I8= (A2,B2,C2)
I9= (A1,B2,C1)I10= (A2,B1,C2)I11= (A2,B2,C2)I12= (A2,B2,C2)
F(A1)k1=0.75F(B1)k1=0.5F(C1)k1=0.25
F(A1)k2=0.75F(B1)k2=0.75F(C1)k2=0.25
F(A1)k3=0.25F(B1)k3=0.25F(C1)k3=0.25
Consider individual I1= (A1,B1,C2)
P(I1 in k1) = (.75)(.5)(.75) = 0.28P(I1 in k2) = (.75)(.75)(.75) = 0.42P(I1 in k3) = (.25)(.25)(.75) = 0.046
Therefore reassign I1 to k2
An exampleBamshad et al (2003) Am. J. Hum. Genet. 72:578-89
But…Bamshad et al (2003) Am. J. Hum. Genet. 72:578-89
Genes mirror geography in EuropeNovembre et al. Nature 456, 98-101
Pharmacogenomics• Many drugs never reach the market because
of side effects in a small minority of patients
• Many drugs on the market are efficacious in only a small fraction of the population
• This variation is (in part) due to genetic determinants – OrissaàEGF mutations– Codeineàcytochrome P450 alleles
Question: Is race, ancestry, ethnicity, geography or genetic substructure a
reasonable proxy for genotype at alleles relevant for drug metabolism?
Answer: So far…No. Still looks as if we will have to genotype the relevant loci before making any guesses
Population genetic structure of variable drug response.
Wilson et al (2001) Nat Genet. 29: 265-269
A = African
B = European
C = Asian
A B CCYP1A2
GSTM1
CYP2C19
DIA4
NAT2
CYP2D6
Evidence for Archaic Asian Ancestry on the Human X ChromosomeGarrigan et al. (2005) Mol. Biol. And Evol. 22:189-192
1) Pseudogene on the X-chromosome2) 18 substitutions between human-chimp3) 15 substitutions between two human alleles4) Assuming a molecular clock the split between
the two human alleles is about 2 million years5) Both alleles found in southern Asia, only one
allele found in Africa6) Only human gene tree to “root” in Asia
Garrigan et al. (2005) Mol. Biol. And Evol. 22:189-192
Garrigan et al. (2005) Mol. Biol. And Evol. 22:189-192
Human evolution in a nutshell
chimpsH. sapien
H. ergaster
H. erectus
H. neanderthalis
5-6 mya
1 mya
0.5 mya
0.2 mya
Human evolution in a nutshell
chimpsH. sapien
H. ergaster
H. erectusH. neanderthalis
5-6 mya
1 mya
0.5 mya
0.2 mya?
So what happened?
1. Strong selection for the Asian allele in southern Asia-not likely since this is a pseudogene locus-fails Tajima’s D test
2. Gene flow between H. sapien and H.erectus in southern Asia
-branch lengths are about right for 2 million years of divergence-H. erectus was in southern Asia until 18,000 years ago
(Morwood et al. and Brown et al. in Nature (2004) vol 431.)
-supporting evidence from genetic analysis of lice and other human parasites (Reed et al (2004) PLoS 2:1972-83)