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Appendix S1. Supplemental methods Table S1. Summary of samples used in the analysis. Sample type refers to biopsy (b), fecal (f), or necropsy (n). Known ID (yes/no) refers to whether the sample is associated with a known whale identified previously through photo‐identification methods. Name refers to either the sample for unknown samples or the whale ID for known samples. Table S2. Summary of observed (H o ) and expected (H e ) heterozygosity and tests for Hardy–Weinberg equilibrium genotypic proportions. Type refers to the type of locus (SNP or STR), P‐value is the P‐value associated with the Hardy–Weinberg test, F IS is Weir and Cockerham's inbreeding coefficient, and alleles is the number of alleles at a locus. Table S3. Summary of paternity inferred from the COLONY analysis. Results from the combined SNP/STR dataset and the SNP‐only dataset are reported. ‘NA’ refers to a failure to assign paternity; ‘conflict’ refers to a difference in paternity assignment between the two datasets (1 = difference, 0 = no difference). Table S4. Comparison of inferred parentage from the COLONY and FRANZ programs. A blank cell means that no sampled parent was identified with a posterior probability > 0.9. ‘Conflict’ refers to a difference between the two methods (1 = difference, 0 = same). Table S5. Summary of paternal half‐sib families from COLONY analysis for the combined (SNP and STR) and SNP‐only datasets. Candidate unsampled males from the southern resident population who were alive and sexually mature the year prior to the births of every member of the half‐sib family are listed as possible fathers (based on the sib‐groups for the combined SNP and STR dataset). ‘P’ refers to the posterior probability of the family group. Table S6. Consensus pedigree based on highly supported (P > 0.90) paternity results and very highly supported (P > 0.95) half‐sib family results from the combined SNP/STR COLONY analysis. Mother‐G refers the mother identified by COLONY; Mother‐F refers the observed mother from field studies, including mothers with no genetic sample in the analysis; Mother‐C refers to the consensus mother (genetically assigned mother if available; field‐assigned mother if not). Table S7. Summary of parentage simulation results, either using field information to exclude potential parents based on age of sexual maturity and known maternal relations (‘use field data’) or ignoring this information (‘no field data’). ‘n’ and ‘n correct’ refer to the number of offspring in the sample and whether the COLONY analysis corrected identified their paternity (‘Father is sampled’) or correctly concluded that the true father was not in the sample (‘Father is not sampled’). Table S8. The effective number of breeders (N b ) estimated by the sibship method of Wang (2009) for samples of southern resident killer whales in 10‐year sliding windows starting with each year in the ‘Year’ column. Samples prior to 1970 are grouped into a single window. Figure S1. Trends in the estimated effective number of breeders (N b ), estimated using the approach of Wang (2009) in a 10‐year sliding window. Dark line is the point estimate and light lines are the 95% confidence intervals based on calculating N b for each of the 1000 highest likelihood configurations from the COLONY analysis. Figure S2. Average (black) and 95% confidence interval (gray) of standardized multi‐locus heterozygosity for the 105 unique samples in the study, based on 68‐94 loci. Values were generated by the ‘sMLH’ function in the inbreedR package, and are the total number of heterozygous loci in an individual divided by the sum of average observed heterozygosities in the population over the subset of loci successfully typed in the focal individual. The two individuals from parent offspring matings are identified by “***” and two more distantly inbred individuals are identified by ‘**’. Figure S3. Density plots of 7 alternative related coefficients for four sets of simulated relationship (full siblings – ‘Full’; half siblings – ‘Half’; parent‐offspring – ‘PO’; and unrelated). The Pearson's correlation coefficient between the estimated and true related value for the simulated pairs ranged from 0.89 to 0.93. All simulations were conducted using the ‘related’ R package (Pew, Muir, Wang et al., 2015). Figure S4. ‐‐ Pairwise estimates of relatedness for full siblings, half‐siblings, parents and offspring, and unknown relationship, using the estimator of Wang (2002). Relationships are based on the consensus pedigree from the study (Table S6). Figure S5. Estimated effect size of standardized MLH on southern resident killer whale survival. Model averaged estimates are generated from weighting competing models with and without MLH included (Model 1 and 2, Table 1). Estimates (with 95% credible interval) are illustrated for a 20‐year‐old female in 2015. In addition to MLH, these models allowed survival to be predicted by age, sex and time. Table S9. – Summary of pod membership of all possible matings and those inferred from the pedigree analysis. Possible matings were based on all possible pairs of males and females who were alive and sexually mature in the same year. The pod membership of inferred matings did not differ significantly from the possible matings (permutation test; X‐square = 7.5458, d.f.= 5, P = 0.18). Table S10. Model fits for alternative GAM models describing survival as a function of time, age, sex and MLH, for population censuses 1979‐2016 and the SNP dataset. To allow comparison between models with and without MLH, the subset of animals with MLH data were used (n = 84). These models either include time as a smoothed term (Y/N), include sex as a fixed effect (‘Factor’, offset) or fits separate splines to age effects by sex (‘Smooth’), and include MLH or not as a predictor (Y/N). The best models (ΔAIC <2) are highlighted in bold. Table S11. Model fits for alternative GAM models describing female killer whale fecundity as a function of time, age and MLH, for population censuses 1979‐2016 and the SNP dataset. To allow comparison between models with and without MLH, the subset of females with MLH data were used (n = 35). The best models (ΔAIC) are highlighted in bold.