ARENT G A E ASSIGNMENT USING PROGRAM CER USING PR

Transcrição

1 PARENTAGE ASSIGNMENT USING PROGRAM CERVUS 3.03 heinzeworld.com

2 Study Background Genetic application to epidemiology Chronic Wasting Disease Prion i disease Fatal Neuro-degenerative

3 Study Background Social groups play a role in CWD transmission Animal animal contact Social interactions Deer social groups consist of related individuals Genetic data can identify familial relationships

4 Walrath l et al. Study Background Behavioral observation of penned deer Examine contact rates between related vs unrelated pairs Unrelated Related Related BAIT

5 Walrath l et al. Study Background Behavioral observation of penned deer Examine contact rates between related vs unrelated pairs But t who s really related?? BAIT

6 Genetic Analysis Goal Use genetic fingerprints Determine relationships between deer Verify y that pairs fit behavioral study design BAIT

7 METHODS

8 Captured Pairs

9 Parentage Assignment A a B B c c d D E E F f a a B b C c d d E e f f 1 allele identical by descent at each locus Potential Parent Several loci with no matching alleles A A B B c c D D E E F F Exclude as Parent

10 Parentage Assignment Who s my mama

11 Parentage Assignment Who s my mama X X X X??

12 CERVUS Marshall, TC, Slate, J, Kruuk, LEB & Pemberton, JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: Slate J, Marshall TC & Pemberton JM (2000) A retrospective assessment of the accuracy of the paternity inference program CERVUS. Molecular Ecology 9: Kalinowski, ST, Taper, ML & Marshall, TC (2007) Revising how the computer program CERVUS accommodates genotyping error paternity Molecular Ecology increases success in p y assignment. g gy 16:

13 TYPES OF ANALYSIS Paternity analysis Mother known OUTCOME most likely father for each offspring Mother unknown Maternity analysis Father known most likely mother for each offspring Father unknown Parent pair analysis Sexes known Sexes unknown most likely parent pair 2 most likely individual parents Simulation analysis Simulate any above confidence in parent assign t

14 TYPES OF ANALYSIS Paternity analysis Mother known OUTCOME most likely father for each offspring Mother unknown Maternity analysis Father known most likely mother for each offspring Father unknown Parent pair analysis Sexes known Sexes unknown most likely parent pair 2 most likely individual parents Simulation analysis Simulate any above confidence in parent assign t

15 Steps Allele l frequency Identity Analysis Simulation Test Parentage Assignment Analysis

16 Input Files - Genotypes Individual ID BM 6506a BM 6506b BM 1225a BM 1225b Na Nb RT 23a RT 23b

17 Input Files - Fawns Offspring ID, Year of birth, Candidate mother IDs

18 1) Allele Frequency Analysis

19 1) Allele Frequency Analysis NEs = non-exclusion probabilities = probability of not excluding an unrelated individual from possibly being a parent

20 2) Identity Analysis

21 2) Identity Analysis

22 2) Identity Analysis

23 2) Recalculate Allele Frequency

24 3) Simulation Tests

25 3) Simulation Tests Critical delta values Note difference with both parents unknown vs one parent tknown

26 4) Parentage Analysis

27 4) Parentage Analysis

28 4) Parentage Analysis Offspring ID Candidate mother ID Loci typed Pair loci compared Pair loci mismatching Pair LOD score Pair Delta Pair confidence E E E E E E E E E E E E E E+0000E E E E E+01 * E E E E E E E E E E+00

29 QUICK REFERENCE GUIDE Allele Frequency Analysis Analysis > Allele Freq. An. > Select genotype file > Indicate row and column properties > Name output file > Select options > OK Identity Analysis Analysis > Identity An. > Select genotype file > Indicate row and column properties > Select allele freq. file > Name output file > Select options > OK Simulation Tests Analysis > Sim. Of Par. An. > Maternity > Select allele freq. file > Set simulation parameters > Name output file > Set confidence levels > OK Parentage Analysis Analysis > Par. An. > Maternity > Select offspring file y y p g > Indicate row and column properties > Indicate parent file if needed > Select genotype file > Select allele freq. & sim. files > Set output options > OK