SR1

Muller’s ratchet and plant evolution: amodeling approach

Peter Pfaffelhuber, Stefan A. Rensing

FRISYS, University of Freiburg

SR2

Editing in plantsEditing in plants

Post-transcriptional change of RNA in semi-autonomous organelles (plastids and mitochondria)

Main function: remedy errors in the DNA code that have occurred through point mutations

Regulatory roles

Compensatory mutations in the nuclear genome: e.g. PPRs (Pentatricopeptide repeat proteins)

e.g., Maier et al. (2008) BMC Biology 6:36

SR3

The mathematical modelThe mathematical model

Assumptions

- infinite population size (Muller‘s ratchet in a finite population has not been solved; this simplification has been used before)

- (mildly) deleterious organellar mutations accumulate over time (rate λ)

- compensatory nuclear mutations occur with a significantly higher rate (γ) (and remedy the organellar mutations and their associated selective disadvantage)

- selection coefficient (s) with multiplicative fitness, i.e. an individual with k deleterious mutations has an offspring distribution with expectation proportional to (1 - s)k

SR4

The model II.The model II.

1 2 3 4 5 6 7 8 9 10 11 12

S1S2

S3

0

200

400

600

800

1000

x

kt

distribution at a given t

distrib

ution ve

ctor

probability measures

on natural numbers

SR5

The model III.The model III.

time derivative

selection gain k -> k+1 compensation k -> k-1

- population in equilibrium

0 < s << λ << γ << 1

- individual: birth-death process

(k<=1 at any t)

time [Ma]

k

lam

bd

a

gam

ma

SR6

Rates per lineageRates per lineage

1.12E-10 chloroplastic1.12E-10 chloroplastic[substitutions per site and year][substitutions per site and year]

Chiang & Schaal (2000) Genome 43:417atpB-rbcL spacer of chloroplast DNA in 11 mosses

9.4E-09 nuclear

Rensing et al. (2007) BMC Evol Biol 7:130

1.5E-8 monocots

6.5E-9 dicotsGaut et al. (1996) PNAS 93:10274

Koch et al. (2000) Mol Biol Evol 17:1483

total gains / 450 Ma per sitelambda estimator

Sphagnum spec 3,0303E-10Takakia lepidozioides 1,0606E-09Pogonatum umigeum 3,2828E-10Diphyscium sessile 1,2626E-10Encalypta streptocarpa 1,0101E-10Leucobryum glaucum 2,2727E-10Timmia bavarica 2,5253E-10Rhacocarpus purpurascens 1,0101E-10Bartramia halleriana 7,5758E-11Splachnum ampullaceum 1,0101E-10Mnium hornum 7,5758E-11Ulota crispa 1,5152E-10

SR7

Rates per time periodRates per time periodEstimate missing nodes using r8s -> finer granularity

Calculate rates per lineage and time interval -> avg. rates per time period

450-380

380-300

300-200

200-100

8.12E-10

2.02E-10

1.37E-10

1.99E-10

100-0

2.22E-10

p < 9E5

SR8

Questions (to be) answeredQuestions (to be) answered

- Can the compensatory mutation hypothesis help to explain why organellar genomes have not deteriorated? YES

- Editing sites are gained with the approximate rate of mutation fixation -> no apparent selective disadvantage

- Are there different rates of gain [and loss] of editing sites (λ) and/or compensatory nuclear mutations (γ) among different lineages that can be derived from the data? YES, for λ (loss and γ pending)

- Are there time periods with differing rates? YES, after the water-to-land transition

SR9

AcknowledgementsAcknowledgements

Freiburg

Andrej Depperschmidt

Peter Pfaffelhuber

Stefan Rensing

Berlin

Michael Tillich