Post on 12-Jan-2016
description
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