From the bare minimum: genetics and selection in populations founded by only a few parents APPENDIX

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1 Evolutionary Ecology Research Volume 17 (2016) From the bare minimum: genetics and selection in populations founded by only a few parents APPENDIX Jacques Labonne 1, Renaud Kaeuffer 2, François Guéraud 1, Mingsha Zhou 2, Aurélie Manicki 1, Andrew P. Hendry 2. 1 INRA, UMR 1224, Ecologie Comportementale et Biologie des Populations de Poissons, Aquapôle, quartier Ibarron, 64310, Saint-Pée sur Nivelle, France. 2 Redpath Museum and Department of Biology, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, H3A 2K6, Canada Corresponding author: Jacques Labonne, labonne@st-pee.inra.fr Running head: HFC in highly inbred populations of Kerguelen Is.

2 Supplementary Information 1: Bayesian Von Bertalanffy model to predict missing ages based on individual total length. 1) likelihood of the Von Bertalanffy model for OPENBUGS Software (reversed to infer effect of total length on age) model { for (i in 1:N) { #length[i]~linf*(1-exp(-k*(age[i]-t0))) # classic model age[i]~dnorm(mu[i],tau)i(0,) mu[i]<-t0-log(1-length[i]/linf)/k # reversed model } # priors tau~dgamma(0.001,0.001) # precision parameter k~ dnorm(0,0.001) # growth rate t0~ dunif(0.5,4) # length range at t=0 Linf~ dunif(80,300) # length at infinity } #example of inits list(linf=85,k=0.1,t0=2,tau=0.1) 2) Data for each population # data for Val Travers population list(age=c(na,4,5,8,6,na,5,4,5,5,5,na,5,5,4,7,5,na,4,6,8,5,1,2,na,2,2,2,na,na,na,1,na,1,na,n A,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,NA, NA,NA,2,NA,2,NA,NA,NA,NA,NA,5,2,4,2,3,2,3,3,3,3,3,2,2,2,NA,2,NA,4,5,4,4,NA,4,6,NA,NA,6,6, NA,5,7,7,7,4,7,6,NA,6,NA,NA,NA,5,8,3,5,6,1,1,1,1,NA,6,5,2,2,1,1,1,1,1,2,2,2,1,2,3,4,1,3,2,3,1,6, 2,2,5,5,2,5,NA,3,2,5,2,2,2,2,2,2,2,1,2,2,2,1,4,2,5,4,4,5,3,3,5,6,1,NA,2,2,1,3,1,1,1,2,3,NA,3,1,1,1, 1,1,9,7), length=c(44.0,27.3,24.7,30.5,26.5,25.7,26.5,29.7,23.4,28.0,25.6,40.9,25.0,23.1,28.5,57.0,38.7, 36.0,22.3,32.5,37.8,29.4,10.3,12.1,7.8,13.5,13.3,13.8,7.8,7.8,8.5,10.7,8.5,16.8,8.6,6.9,7.4,7.9,7.3,8.4,8.5,5.9,6.2,7.4,6.6,6.6,6.6,7.2,6.3,8.2,6.2,6.3,10.4,7.5,7.8,7.6,7.4,7.2,7.0,6.6,7.1,7.2,8.0,7.0,12.3,6.4,10.2,6.9,7.1,8.3,7.1,7.0,21.7,11.8,19.2,13.0,14.5,12.3,11.5,15.7,19.1,15.4,14.8,14.1,

3 16.0,12.0,8.7,18.0,29.0,22.5,23.0,24.5,23.5,9.6,25.0,36.0,8.0,9.4,28.0,48.0,47.8,45.0,43.0,46.8, 52.5,46.7,46.3,46.0,47.0,48.5,51.0,43.0,46.0,51.0,44.0,15.4,23.0,23.3,7.4,10.0,9.6,7.8,25.3,27. 0,28.0,13.7,14.3,10.5,8.4,11.0,9.2,16.0,12.2,8.9,12.9,7.5,13.6,14.7,23.7,7.9,16.8,9.3,18.8,7.8,3 1.0,10.7,10.8,22.8,23.5,13.3,24.3,14.7,17.9,14.0,26.4,12.6,14.6,14.1,8.7,8.2,8.5,8.8,10.1,12.0,1 0.0,10.3,8.9,18.5,9.4,36.5,18.3,22.0,21.8,18.2,24.5,19.5,21.0,9.6,10.5,8.4,13.8,10.8,19.0,7.0,9. 0,10.2,12.4,11.8,18.8,17.5,8.1,9.2,11.1,11.0,9.8,40.0,40.5), N=197) # data for Clarée population list(age=c(5,1,4,2,8,7,8,1,1,3,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,1,1,1,1,1,1,1,1,1,1,1,1, 1,1,1,1,1,1,1,1,1,2,3,NA,2,1,NA,2,1,1,1,1,NA,1,1,2,1,1,2,NA,1,2,1,1,2,1,NA,1,1,2,NA,1,1,NA,1,1, NA,NA,NA,NA,NA,NA,5,NA,NA,NA,8,6,6,6,NA,NA,NA,6,5,7,4,3,5,5,5,5,9,5,5,NA,1,7,1,6,1,6,2,6, NA,8,6,7,2,5,1,6), length=c(40.5,13.5,29.4,11.3,62.0,60.5,60.0,15.7,16.5,17.5,13.2,15.8,15.0,11.5,12.3,13.4,13.6, 14.7,14.1,12.9,11.8,14.6,17.0,17.8,10.9,11.9,13.2,12.4,10.5,12.8,10.1,18.0,13.1,10.4,11.1,11.6, 11.3,12.0,10.7,13.7,12.2,9.1,13.3,12.9,13.9,11.3,11.4,12.8,11.9,12.5,10.3,12.1,9.8,10.6,19.0,20.2,11.9,14.2,13.9,10.5,14.8,12.5,13.4,11.5,13.1,11.1,14.9,15.4,12.3,13.0,11.1,19.6,10.2,13.5,14.3,16.5,17.5,9.7,13.8,10.4,13.0,16.9,16.9,9.7,13.2,18.0,8.1,16.0,15.0,11.1,9.7,10.9,8.7,9.5,10.1, 42.2,10.1,9.4,13.4,57.0,42.1,44.5,54.5,49.0,49.0,45.5,38.5,46.0,48.5,29.0,21.5,47.0,31.0,45.5,6 2.0,72.5,58.0,60.0,10.6,14.3,46.6,13.2,38.0,12.5,48.3,14.5,41.3,15.4,51.4,58.3,66.0,16.3,41.0,1 4.8,46.0), N=135) 3) Estimates of posterior distributions of hyperparameters for each population. For Val Travers: Hyperparameter mean sd Linf k t tau For Clarée: Hyperparameter mean sd Linf k t tau

4 4) Estimates of posterior distributions of missing ages for each population. For Val Travers: age[individual] Mean SD age[1] age[6] age[12] age[18] age[25] age[29] age[30] age[31] age[33] age[35] age[36] age[37] age[38] age[39] age[40] age[41] age[42] age[43] age[44] age[45] age[46] age[47] age[48] age[49] age[50] age[51] age[52] age[54] age[55] age[56] age[57] age[58] age[59] age[60] age[61] age[62] age[63] age[64]

5 age[66] age[68] age[69] age[70] age[71] age[72] age[87] age[89] age[94] age[97] age[98] age[101] age[109] age[111] age[112] age[113] age[123] age[152] age[179] age[189] For Clarée: mean sd age[57] age[60] age[66] age[73] age[80] age[84] age[87] age[90] age[91] age[92] age[93] age[94] age[95] age[97] age[98] age[99] age[104] age[105] age[106] age[119] age[128]

6 Supplementary Information 2: Microsatellite markers information. Marker names Length range (bp) Linkage group Linked genes Maximum allele number known multiplex A multiplex B multiplex C multiplex D Ssa SEX 9 à 15 SsaD ? * 33 StrUBA ? MHC 10 à 15 OmyRT5U SEX? Ss * 20 Ssa103NVH *? SSOSL *? Str * 43 SSOSL ? * 24 SsaT47Lee /19 * 23 Ssa121NVH * 31 SSOSL * 21 T ? *? Ssa179NVH * 30 Ssa159NVHH * 29 SSOSL * 19

7 Supplementary Information 3: Polymerase chain reaction protocols. A) Four multiplexes (A, B, C, D) were created with four markers to avoid superposition of similar sized alleles of different markers during genotyping (Supplementary Information 2). PCRs were carried out in 5µL of final volume using Qiagen Hotstartaq Master Mix kit. Each reaction contained 1X PCR Master Mix, 0.2 to 1.2 µm of labeled primer, and approximatively 25 ng of template DNA. Reactions were carried out on a 2720 thermalcycler (Life Technologies) and consisted of an initial denaturation at 96 C 15 minutes, followed by 5 cycles of denaturing at 96 C for 1 min, annealing for 30 sec, extension at 72 C for 30 s, then 30 cycles of denaturing at 96 C for 30 sec, annealing for 30 sec, extension at 72 C for 30 s, and a final extension step at 72 C for 45 min. Multiplex A had an annealing temperature of 54 C, multiplex B and D of 52 C, and multiplex C of 50 C (Gharbi et al. 2006). B) PCR reactions were performed in multiplex in a final volume of 10 µl using Qiagen Hotstartaq Master Mix kit, with 1 X PCR Master Mix, 0.2 µm of each unlabeled primer and approximatively 25 ng of template DNA. Reactions were carried out on the same thermalcycler (2720, Life Technologies) and consisted in an initial denaturation at 95 C for 15 minutes, and then 30 cycles of denaturing at 94 C for 1 min, annealing at 52 Cfor 1 min, extension at 72 C for 30 s and a final extension step at 72 C for 7 min. PCR products were visualized on an 8% acrylamide gel.

8 Supplementary Information 4: Population genetics indicators For Val Travers and Clarée populations, allelic diversity (k), number of successfully genotyped individuals (N), observed heterozygosity (H obs ), expected heterozygosity (H exp ), tests for Hardy- Weinberg equilibrium (HW), and estimates of null allele frequency (Null). Val Travers Locus k N H obs H exp HW Null OmyRT5U p= STRUBA p= *** Ssa p= SSAD p= SS p= SSOSL p< *** SSA103NVH p= STR p= SSOSL p= SSOSL p= SSA121NVH p= SSAT47LEE p= SSOSL p= SSA159NVH p= SSA179NVH p= T p= Clarée Locus k N H obs H exp HW Null OmyRT5U p= STRUBA p< *** Ssa p= SSAD p= SS p= SSOSL p= SSA103NVH p= STR p=

9 SSOSL p= SSOSL p= SSA121NVH p= SSAT47LEE p= SSOSL p= SSA159NVH p= SSA179NVH p= T p=

10