Incongruency between demographic-based and genetic-based estimates of effective population size

Marco Andrello, M Gaudeul, I Till-Bottraud and O.E Gaggiotti

Modèles en Ecologie Evolutive, Montpellier, 31st May - 2nd June 2010

Definition

Use of Ne

– in conservation– In evolutionary ecology

Estimation methods for Ne

Assessment of estimators:– different approaches give inconsistent estimates– Why??

Definition

pt allele frequency at time t

tt ppp 1 0pE N

pppVar tt

2

1

Wright-Fisher population:DiploidyHermaphroditismSelf-compatibilityDiscrete generationsRandom matingNo migrationNo mutationNo selectionVariance in reproductive success: Poisson

No Wright-Fisher:

e

tt

N

pppVar

2

1

Ne is size of an ideal (Wright-Fisher) population that undergoes the same amount of gene frequency change as the population under consideration

Use of Ne in conservation biology

• Inbreeding

• Loss of genetic variation

• Accumulation of slightly deleterious mutations

12

11

2

1

t

eet F

NNF

eNtHtH

2

11)()1(

eNs

2

1

Use of Ne in evolutionary biology

• Allele fixation

• Genetic variability

• Adaptation

efix Nt 4

e

e

N

NH

41

4~

Estimation of Ne: demographic methods

– Fluctuating population size

– Overlapping generationsYonezawa et al. 2000

L

t t

e

N

LN

1

1

LV

NNe

12

k

VuuuV k 11112 2

Estimation of Ne: genetic methods

• Temporal methodWaples 1989

• Single-sample estimators– Linkage disequilibrium LDNe

Waples&Do 2008

– Bayesian ABC ONeSAMPTallmon et al. 2008

NSSF

tN

tke /12/12/12 0

SrNe /1ˆ3

12

,...~ , HLD, FN ISe

Do the two approaches give the same estimates?

Eryngium alpinum Overlapping generationsStage structureVariance in reproductive success

Demographic and genetic data for 4 populations:2001 – 2009 demographic surveyGenetic samples; 8 microsatellites

Ne estimation:LDNeONeSAMPDemographic

Yonezawa et al. 2000

Le V

NN

/11

12 20

LDNe does not provide upper CI: small sample sizegood precision with n·L·K ≈ 1000we have n·L·K ≈ 722

Negative LDNe estimate: insufficient information in the sample

Ranking of populations– demographic: follows Nh, different Ne per population– ONeSAMP: populations have the same Ne

Why the demographic and the ONeSAMP method give different estimates?

1

10

100

1 000

10 000

100 000

1 000 000

10 000 000

Deslioures Pralognan Bernards Boujurian

Nh

Demographic

LDNe

ONeSAMP

SrNe /1ˆ3

12

1. Demographic and genetic methods might measure different things

2. Potential biases of the demographic method

3. Bias of genetic methods?

1

10

100

1 000

10 000

100 000

1 000 000

10 000 000

Deslioures Pralognan Bernards Boujurian

Nh

Demographic

LDNe

ONeSAMP

Demographic and genetic methods might measure different things– Genetic Ne: realized drift

Demographic Ne : future drift• accounts only for modelled processes!

– Sampling periods: should be consistent• Demographic data 2001-2008• Genetic samples: 2001

= 1.04 = 0.92

Potential biases of the demographic method– population size

population growth rate– estimation of reproductive success: variation in

realized fecundity (Heywood 1986)

– Parameters are estimated with uncertaintyHeywood model assumes random recruitment from the seed pool!

2

22

2

2

2

1

11

b

bk

B

b

b

k

Bb

kbk N

N

Le V

NN

/11

12 20

k

kuuuV

22 11112

mean number of seeds

variance in number of seeds

mean number of seedlingsk

b

b

2

Bias of the genetic methods?• ONeSAMP never tested for accuracy and precision

– Saarinen et al. (2009): ONeSAMP and LDNe give comparable, but different, results

– Beebee (2009): ONeSAMP and sibship assignment method (Wang 2009) give similar results

• But are those estimates reliable? Need for a simulation study considering variable numbers of loci, polymorphism, life-histories and sample sizes– ONeSAMP is web based and is hard to conduct such a study

Conclusions and perspectives

• Ne is an important parameter, but still difficult to estimate

• Demographic and genetic methods gave inconsistent results

• Use large sample size to get precise genetic estimates

• Conduct an assessment of ONeSAMP• Extend comparisons to more species for which

demographic data are available• Use different methods when possible!