Variation in the molecular clock of primates
Priya Moorjani*, Carlos Eduardo G. Amorim*, Peter F. Arndt, Molly Przeworski
Molecular Clock Used for dating evolutionary events under the assumption that genomic changes at neutral sites occur at a constant rate per unit time (so clock-like)
Human Neanderthal Chimpanzee Orangutan Macaque
Zuckerkandl and Pauling 1965, Kimura 1983, Kumar 2005
Neutral theory Substitution rate = mutation rate
Divergence time (Myr)
13
35
1.4
mutations
Variation in substitution rates among mammals
Wu and Li 1985, Sayres et al. 2011, Hwang and Green 2004
Accumulation of mutations with sex and age
Ségurel et al. 2014; Gao et al. 2016
Parental Age
# of replication driven mutations
Puberty (P) Birth
male
female
Mean age of reproduction (G)
Pre-‐puberty Post-‐puberty Prenatal
Conception
combined
d1 , μ1
d2 , μ2
d0 μ0
di = number of cell divisions in stage i μi = mutation rate per cell division in stage i
Different yearly mutation rates expected for distinct life histories
# of replication driven mutations
Puberty (P) Birth Generation time (G) Conception
Yearly mutation rate: μy = 0.4 x 10-‐9 per bp
G = 11y P = 3.5y μy = 0.7 x 10-‐9
G = 6y P = 0.9y μy = 1.2 x 10-‐9
d1 , μ1
d2 , μ2
d0 , μ0
G = 29y P = 13y
Amster and Sella 2016 Kong et al. 2013
How much variation in the molecular clock is there among primates?
Data analysis
Phylofit (Siepel and Haussler 2004)
Maximum Likelihood approach
(Duret and Arndt 2008)
Substitution count matrix
(accounting for mutation context)
Lineage-specific
substitution rates
§ Multiz: 10 primate alignment (Murphy et al. 2001) § EPO: 7 primate alignment (www.ensembl.org)
+
Putatively neutral substitution rates in primates
human
chimpanzee
orangutan
rhesus macaque
crab−eating macaque
baboon
green monkey
marmoset
squirrel monkey
bushbaby
mouse
ApesOld World MonkeysNew World MonkeysProsimiansOutgroup
Whole genome alignments (MultiZ); to focus on putatively neutral sites, we removed conserved elements, exons and transposable elements.
OWM−Hominoid: 1.37
human: 1.00
chimpanzee: 1.01
orangutan: 1.04
rhesus macaque: 1.42
crab−eating macaque: 1.41
baboon: 1.37
green monkey: 1.36
0.005
Apes vs monkeys
Consistent with hominoid rate slowdown Goodman 1962
NWM−Hominoid: 1.64
human: 1.00
chimpanzee: 1.01
orangutan: 1.03
marmoset: 1.66
squirrel monkey: 1.65
0.01
G= 25-29 y P = 13 y
G = 6-9 y P = 1-3 y
G= 25-29 y P = 13 y
G= 11-12 y P = 3.5 y
*
Differences within apes
human
chimpanzee
orangutan
0.621%
0.633%
G = 25 y P = 8.5 y
G = 29 y P = 13 y
Chimp branch is +1.9% compared to human
High Coverage human (~30x), chimpanzee (~30x) (Venn et al. 2014) and gorilla (~30x) (Prado-Martinez et al. 2013) mapped to orangutan reference genome; substitution matrix estimated by Phylofit
human
gorilla
orangutan
0.773%
0.824%
G = 19 y P = 6.5 y
G = 29 y P = 13 y
Gorilla branch is +6.6% compared to human
Not all substitution types behave similarly
Hwang and Green 2004
Distance from root to leaf
CpG transitions
Mutations have different possible sources Replication-driven Non-replicative in origin
5’ methylated cytosine thymine
Gao et al. 2016
efficient repair inefficient repair
Mutation rate should have less dependence on life history traits
#"of"mutations"
Puberty"(P)"Birth"
male"
female"
Generation"time"(G)"
Pre7puberty" Post7puberty"Prenatal"
combined"
Conception"
Mutation rate depends on life history traits
#"of"mutations"
Puberty"(P)"Birth"
male"
female"
Generation"time"(G)"
Pre7puberty" Post7puberty"Prenatal"
combined"
d1 , µ1
d2 , µ2
d0 µ0
Conception"
Likely non-replicative in origin
CpG transitions 1.07
human: 1.00
chimpanzee: 1.01
orangutan: 1.00
rhesus macaque: 1.08
crab−eating macaque: 1.06
baboon: 1.08
green monkey: 1.07
0.05
Hwang and Green 2004, Kim et al. 2006
Thought to be due to replication errors
G= 25-29 y P = 13 y
G= 11-12 y P = 3.5 y
non−CpG G/C transitions 1.38
human: 1.00
chimpanzee: 1.01
orangutan: 1.11
rhesus macaque: 1.43
crab−eating macaque: 1.40
baboon: 1.45
green monkey: 1.47
0.005
*
human
chimpanzee
orangutan
rhesus macaque
crab−eating macaque
baboon
green monkey
marmoset
squirrel monkey
● ●
●
●
●
●
0.00
0.02
0.04
0.06
Roo
t−le
af v
aria
nce
●
●
●
●
●
●
A/T G/C CpG outside CpG island (CGI)
CpG in CGI
non−CpG G/C outside CGI
non−CpG G/C in CGI
●
●
transitionstransversions
Deviation from clock-like behavior by substitution type
Distance from root to leaf
*
mostly methylated
mostly unmethylated
likely non-replicative
in origin
likely due to errors in
replication
Not only do mutation rates evolve, so does the spectrum
human chimpanzee orangutanrhesus
macaquecrab−eating
macaque baboongreen
monkey marmosetsquirrelmonkey
Frac
tion
of s
ubst
itutio
ns0.
000.
050.
100.
150.
200.
250.
30
A/T transitionsA/T transversions
non−CpG G/C transitionsnon−CpG G/C tranversions
CpG transitionsCpG transversions
● ●
●
●
●
●
0.00
0.02
0.04
0.06
Roo
t−le
af v
aria
nce
●
●
●
●
●
●
A/T G/C CpG outside CpG island (CGI)
CpG in CGI
non−CpG G/C outside CGI
non−CpG G/C in CGI
●
●
transitionstransversions
v Variation in substitution rates depends upon the source of the mutation.
Implications for molecular clock v There is substantial variation in the molecular clock across primates.
v Challenge for dating for evolutionary events in primates. v Model the impact of life history traits on substitution rates (Amster and Sella 2016) v Use a more clock-like set of substitutions such as CpG transitions for dating.
Using CpG transitions only
Assuming ancestral population size (Na) = 5* current population size (Nh) at CpG transitions HG split time: 10.8 Mya HC split time = 7.9 Mya
Wall 2002, Prado-Martinez et al. 2013
Assuming pedigree-based per year mutation rate at CpG transitions from Kong et al. 2012
Human−chimpanzee divergence:12.1 Mya
human
chimpanzee
orangutan
4.784%
4.917%
Human−gorilla divergence: 15.1 Mya
human
gorilla
orangutan
5.939%
6.341%
Acknowledgments
Thanks for helpful discussions: Minyoung Wyman, Guy Amster, Guy Sella, Nick Patterson, Heng Li, Adam Siepel, Melissa Hubisz, David Pilbeam and members of Przeworski lab
C. Eduardo Amorim Peter Arndt Ziyue Gao Molly Przeworski
NIH and Ruth L. Kirschstein National Research Service Postdoctoral Award
Pre-print: http://www.biorxiv.org/content/early/2016/01/11/036434