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Supplementary material reporting R code for the manuscript ‘Stronger net selection on males across animals’.

Phenotypic gambit

Statistical analyses were carried out in two steps. First, we examined the key assumption of the ‘phenotypic gambit’ by testing whether estimates of phenotypic variance predict the estimated genetic variance. For this we computed the Pearson correlation coefficient r, testing the relationship between CVP and CVG for both sexes and the two fitness components separately. In addition, we tested whether the sex bias in CVP translates into a sex bias in CVG by correlating the coefficient of variation ratio lnCVR (Nakagawa et al. 2015), which refers to the ln-transformed ratio of male CV to female CV, with positive values indicating a male bias. The analyses on the phenotypic gambit were motivated from a methodological perspective and we did not expect that inter-specific variation in the difference between CVP and CVG can be explained by a shared phylogenetic history. However, for completeness, we also ran correlations on phylogenetic independent contrasts (PICs; computed using the ape R-package (version 5.4.1) in R (Paradis & Schliep 2019)) to test whether our findings were robust when accounting for potential phylogenetic non-independence. We report Pearson’s correlation coefficients r for normally distributed data and Spearman’s rho if assumptions of normality were violated.

MCMC APPROACH - Reproductive Success


 Iterations = 100001:1099501
 Thinning interval  = 500
 Sample size  = 2000 

 DIC: 50.043 

 G-structure:  ~animal

       post.mean  l-95% CI u-95% CI eff.samp
animal   0.02255 0.0002015  0.07153     2000

               ~Index

      post.mean l-95% CI u-95% CI eff.samp
Index   0.06268 0.002205   0.1299     2000

               ~Study_ID

         post.mean  l-95% CI u-95% CI eff.samp
Study_ID   0.05648 0.0003111    0.144     2000

 R-structure:  ~units

      post.mean l-95% CI u-95% CI eff.samp
units    0.0598  0.03933  0.08289     2241

 Location effects: phenCV ~ factor(Sex) 

                       post.mean l-95% CI u-95% CI eff.samp  pMCMC    
(Intercept)               0.6941   0.4875   0.8888     2000 <5e-04 ***
factor(Sex)phenCV_male    0.2329   0.1500   0.3183     2000 <5e-04 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggplot2_3.3.3              data.table_1.14.0         
 [3] stargazer_5.2.2            dplyr_1.0.5               
 [5] MCMCglmm_2.32              coda_0.19-4               
 [7] tidyr_1.1.3                PerformanceAnalytics_2.0.4
 [9] xts_0.12.1                 zoo_1.8-9                 
[11] matrixcalc_1.0-3           outliers_0.14             
[13] psych_2.1.3                multcomp_1.4-16           
[15] TH.data_1.0-10             survival_3.1-12           
[17] mvtnorm_1.1-1              pwr_1.3-0                 
[19] MASS_7.3-51.5              metafor_2.4-0             
[21] Matrix_1.2-18              ape_5.4-1                 
[23] workflowr_1.6.2           

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        lattice_0.20-41   corpcor_1.6.9     assertthat_0.2.1 
 [5] rprojroot_2.0.2   digest_0.6.27     utf8_1.2.1        R6_2.5.0         
 [9] evaluate_0.14     highr_0.8         pillar_1.5.1      rlang_0.4.10     
[13] cubature_2.0.4.1  whisker_0.4       rmarkdown_2.7     splines_4.0.0    
[17] stringr_1.4.0     munsell_0.5.0     compiler_4.0.0    httpuv_1.6.1     
[21] xfun_0.22         pkgconfig_2.0.3   mnormt_2.0.2      tmvnsim_1.0-2    
[25] htmltools_0.5.1.1 tidyselect_1.1.0  tibble_3.1.0      tensorA_0.36.2   
[29] quadprog_1.5-8    codetools_0.2-16  fansi_0.4.2       withr_2.4.1      
[33] crayon_1.4.1      later_1.2.0       grid_4.0.0        gtable_0.3.0     
[37] nlme_3.1-147      lifecycle_1.0.0   DBI_1.1.1         git2r_0.28.0     
[41] magrittr_2.0.1    scales_1.1.1      stringi_1.5.3     fs_1.5.0         
[45] promises_1.2.0.1  ellipsis_0.3.1    vctrs_0.3.6       generics_0.1.0   
[49] sandwich_3.0-0    tools_4.0.0       glue_1.4.2        purrr_0.3.4      
[53] parallel_4.0.0    yaml_2.2.1        colorspace_2.0-0  knitr_1.31