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