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Lecture 6

Lecture 6. VII. Real and published examples. Borrelia valaisiana. B. garinii. B. afzelii. B. burgdorferi. B. Spielmanii. 1. Population genetics of Ixodes ricinus and Lyme borreliosis in Switzerland. 0.7. 0.6. 1. 0.5. estimator). 0.4. 0.75. 0.3. is. F. (. 0.5. f. 0.2.

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Lecture 6

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  1. Lecture 6

  2. VII. Real and published examples

  3. Borrelia valaisiana B. garinii B. afzelii B. burgdorferi B. Spielmanii 1. Population genetics of Ixodesricinus and Lyme borreliosis in Switzerland

  4. 0.7 0.6 1 0.5 estimator) 0.4 0.75 0.3 is F ( 0.5 f 0.2 0.1 0.25 0 (partials) 0 IR8 IR25 IR27 IR32 IR39 All is F -0.25 -0.5 -0.75 -1 109 111 113 115 117 119 121 123 125 127 129 131 Allele size Heterozygote deficits

  5. B. valaisiana B. afzelii B. burgdorferi B. garinii Sex specific allocation of polymorphism Sex biased dispersal in ticks?

  6. Borrelia detection in ticks For Borrelia burgdorferi P =0.012 ss 0.08 0.07 B. burgdorferi 0.06 0.05 0.04 Prévalence of 0.03 0.02 F M Sex of the tick

  7. Borrelia detection in ticks For Borrelia afzelii Uninfected Infected Uninfected Infected

  8. 2. Candida albicans in Abidjan (Ivory Coast) 14 enzymatic loci 42 AIDS Patients FPatient≈0.5 (P<0.001) 23 males 19 females FSex≈0.08 (P<0.02) Fis=-0.97 Fis=-0.66

  9. Clones structured in numerous demes

  10. Population genetic structure of Candida albicansin HIV+patients from Ivory Coast Nm=0.09 Nm=0.01

  11. Conclusions

  12. Sampling design: a key and though too often neglected factor -Sampling individuals belonging to the same cohort -Balanced sub-sample sizes as much as possible -At least 20 individuals per sub-sample is desirable, but not less than 5 - At least 5 sub-samples but rather 10 -Tackling, as much as possible, all factors that are susceptible to play a role and GPS recording in any case

  13. Sampling design: a key and though too often neglected factor -Sampling individuals at different dates in the same sites, taking into account the generation time (at least 1 generation between the two sampling campaigns). t1 t1+x

  14. The choice of molecular markers to be used is key - Diploid - Codominant - Autosomal - Not less than 5, 10-20 is much better - Dinucleotidic microsatellite markers (non coding) theoretically represent the best value for money - SNPs much more expensive, maximum homoplasy, may be coding, bias-generating selection process - RFLP expensive and DNA greedy - MLST expensive and coding - Null alleles should be avoided - Allelic dropout should be avoided - Stuttering should be avoided - Short allele dominance should be avoided - Never leave a FIS>0 unexplained - Check the consistency of each marker with the others - Never hesitate getting rid of some outlier loci Haploid markers (or organisms) do not give access to local structure (no information on heterozygosity )

  15. Analyses to be undertaken - Give priority to multi-locus analyses that are more powerful and easier to interpret (a single value, a single P-value) - Get rid of linkage disequilibrium analysis first - Analyze then the local structure but after making sure of the actual level at which the smallest demographic unit (sdu) is located - Analyze differentiation at the different available known levels - Use paired differentiation tests only if no other solution exists, and then do it following a planned design (only use the most relevant sdu's for these comparisons) in order to limit power loss resulting from corrections of the level of significance (Bonferroni) - Never pool heterogeneous sdu's: Methods using individuals (e.g. isolation by distance between individuals) or high rank hierarchies exist - Think hard about what is the highest risk made while taking the final decision for choosing between H0 and H1 - Think hard what is the biological meaning of H0 and H1 Never hesitate to ask for help from people with better skills than yours in one domain or the other: this is the job for which they get their pay check (in theory)

  16. Thank you for your attention and for your patience

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