Lab Exercise: Paternity Analysis

Oct 18, 2006

Plan For TodayFour groups each with different data set

Separate instructions for each group

Two paternity analysis programs:

Cervus for likelihood-based methodVelko for 'modified exclusion'

Determine paternity and 'gene flow' with each method

Determine how outcomes change with different parameters

Measuring gene flow by paternity exclusion

b = observed gene flow (no compatible genotype)

d = Pr (distinguishing immigrant genotype)

Local population Background

b = md

Cryptic gene flow = m(1-d)

^m= ^ __

^b

d

Likelihood Approach to Paternity Assignment

Marshall et al. (1998)

where H1 is probability male a is father,H2 is probability male a is not father

T is transition probabilityand go,gm and ga are genotypes of offspring, mother,

and alleged father, respectively

Cervus and Likelihood

Incorporates genotyping error into likelihood calculation

All males have SOME possibility of being true parentBased on observed error rates averaged across loci

Determines "critical value" (∆) based on difference in LOD between two most likely parents

Simulated populations based on observed allele frequenciesIncorporates incomplete sampling and missing data

Marshall et al. (1998)

North Atlantic humpback whales in the West Indies

No. of females 145

No. of offspring 146

No. of males 348

No. of loci 6

Polygamous

Males compete by ‘singing’ and form groups of primary escorts, challengers, and secondary escorts

Acer Laptop

Douglas-fir seed orchard in Oregon

No. of mother trees 16

No. of seeds 576

No. of candidate parents 59

No. of loci 9

Monoecious, highly outcrossed, extensive pollen flow

Seed orchards contain genetically superior trees for seed production

Pollen immigration is a big problem

Wild Deer (Cervus elatus), Isle of Rum

No. of mothers 49

No. of offspring 49

No. of candidate parents 66

No. of loci 9

Isolated island with rare immigration

High inbreeding

Nine microsatellite loci

Populus trichocarpa Eastern Oregon (Vinson)

Completely outcrossing (dioecious)

Huge effective population size, extensive gene flow (presumably)

Ten SSR loci

12 populations, 22 mothers, 664 progeny

Gateway Desktop

10 km

Vinson Populations

Vinson

Lab Results

Allowing mismatches decreases exclusion power and geneflow estimates

Proportion of population sampled has drastic effect on Cervus

Cervus doesn't work well for estimating gene flow

Douglas-fir most robust, whales least powerful

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Gene FlowAmbiguous PaternitiesSingle Paternities

Deer Douglas-fir Poplar WhalesNumber of Mismatches for Exclusion

Velko Modified Exclusion Analyses

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0.1 0.5 1 0.1 0.5 1 0.1 0.5 1 0.1 0.5 1Deer Douglas-fir Poplar Whales

Proportion of Fathers Sampled

Cervus Likelihood Analyses

Vinson

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Misma t c he s a llowe d

Lab Results: Comparison of Male Fecundities

Excellent correspondence for Douglas-fir: Gancho rocks!

No correspondence for whales: low power, especially for Cervus

Cervus usually overestimates fecundity, sometimes drastically

Deery = 1.3793x

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Exclusion, 2 mismatches

Cer

vus,

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pled

Douglas-Firy = 0.7378x

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Exclusion, 3 Mismatches

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Poplary = 1.3056x

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Exclusion, 3 Mismatches

Cer

vus,

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Whales

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Exclusion, 2 mismatches

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