Online Resource 11St-Onge Et Al. 2015

Online Resource 11 St-Onge et al. 2015

Title: Tracking larvae with molecular markers reveals high relatedness

and early seasonal recruitment success in a partially spawning

marine bivalve

Authors: Philippe St-Onge1*, Réjean Tremblay1 and Jean-Marie

Sévigny2

Institutional affiliations: 1Institut des Sciences de la Mer, Université du Québec à Rimouski,

310 Allée des Ursulines, Rimouski, QC, Canada G5L 3A1 ;

2Pêches et Océans Canada, Institut Maurice-Lamontagne, 850

Route de la Mer, Mont-Joli, QC, Canada, G5H 3Z4

*Corresponding author: Centro de Biologia Marinha (CEBIMar), Universidade de Sao

Paulo (USO), Rodovia Doutor Manuel Hypolito do Rego

km.131,5, Bairro Praia do Cabelo Gordo, Sao Sebastiao, SP,

Brazil, CEP : 11600-000, Tel : (12) 3862-8448; Fax : (12) 3862-

1842, [email protected]

Submission date: June 6th 2014

Final resubmission date: January 12th 2015

Author Contributions: PS conceived the experiments. PS, RT and JMS designed the

experiments. PS performed the experiments and analyzed the data.

PS, RT and JMS wrote the manuscript

Online Resource 11 Estimated number of breeders (NB) responsible for producing all individuals in each sample. Estimates (with 95% confidence intervals) were generated using the linkage disequilibrium (LD) Online Resource 11 St-Onge et al. 2015 method (Waples and Do 2008), the heterozygote excess (HE) method (Zhdanova and Pudovkin 2008), the molecular coancestry (MC) method (Nomura 2008) and the sibship assignment (SA) method (Wang 2009). All LD, HE and MC estimates were calculated as implemented in the NEESTIMATOR v.2.0 software (Do et al. 2014) while all SA estimates were calculated as implemented in the COLONY v.2.0.2.2. software (Jones and Wang 2010).

Linkage Heterozygote Molecular Sibship Disequilibrium Excess Coancestry Assignment (LD) (HE) (MC) (SA) E1 278.3 ∞ 11.2 20.0 (27.4 – ∞) (30.5 – ∞) (5.5 – 19.0) (11.0 – 39.0) E2 1425.5 ∞ 164.4 33.0 (49.9 – ∞) (∞ – ∞) (0.2 – 825.3) (19.0 – 65.0) E5 ∞ ∞ ∞ 19.0 (27.1 – ∞) (17.9 – ∞) (∞ – ∞) (7.0 – 402.0) L3 ∞ ∞ ∞ 17.0 (33.3 – ∞) (20.7 – ∞) (∞ – ∞) (8.0 – 47.0) L4 ∞ ∞ 11.9 32.0 (205.6 – ∞) (∞ – ∞) (0.3 – 44.0) (19.0 – 56.0) L6 ∞ ∞ ∞ 17.0 (274.1 – ∞) (40.1 – ∞) (∞ – ∞) (9.0 – 36.0) P3 1809.9 ∞ 14.9 28.0 (90.8 – ∞) (35.0 – ∞) (2.5 – 38.3) (16.0 – 50.0) P5 431.8 ∞ 91.3 39.0 (82.3 – ∞) (27.5 – ∞) (0.1 – 458.5) (24.0 – 73.0) P8 ∞ ∞ ∞ 27.0 (63.6 – ∞) (∞ – ∞) (∞ – ∞) (15.0 – 49.0) P10 ∞ ∞ ∞ 34.0 (45.2 – ∞) (16.3 – ∞) (∞ – ∞) (15.0 – 202.0) A ∞ ∞ 318.5 53.0 (303.1 – ∞) (32.2 – ∞) (0.3 – 1599.1) (34.0 – 87.0)

References Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR (2014) NEESTIMATOR v2: re- implementation of software for the estimation of contemporary effective population size (N-e) from genetic data. Mol Ecol Resour 14:209-214 Jones OR, Wang JL (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10:551-555 Nomura T (2008) Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evol Appl 1: 462-474 Wang J (2009) A new method for estimating effective population sizes from a single sample of multilocus genotypes. Mol Ecol 18(10): 2148-2164 Wang JL (2011) COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol Ecol Resour 11(1): 141-145 Waples RS, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8(4): 753-756 Zhdanova O, Pudovkin AI (2008) Nb_HetEx: a program to estimate the effective number of breeders. J Hered 99: 694-695