Data from: Asymmetry in cross-sex cross-trait genetic covariances and the evolvability of sexual dimorphism
Abstract
The evolution of sexual dimorphism is predicted to resolve conflict that can arise from divergent evolutionary interests between sexes, enabling each sex to reach its fitness optimum. However, most of the genome is shared between sexes, which can lead to a genetic constraint for dimorphism evolution. Most studies of intersexual genetic constraints have focused on the effect of genetic correlations, rmf, for single traits. However, multivariate studies of the B-matrix of intersexual genetic covariances suggest that sexual dimorphism may be more evolvable than inferred from rmf because of the potential for indirect responses to selection from correlated traits. To comprehensively address this question, we collected and re-analyzed published estimates of B using a recently developed approach to quantify the evolvability of sexual monomorphism and dimorphism. We find that across the traits and species we study, the evolvability of dimorphism is lower than that of monomorphism, but also that sexually concordant and antagonistic selection are almost equally capable of producing dimorphism. We also find that asymmetry in B would affect the response to selection more in females than in males. Our results show that sexual dimorphism is more evolvable than studies of rmf suggest and underscore that sexually antagonistic selection is not required for the evolution of sexual dimorphism.
Dataset DOI: 10.5061/dryad.sxksn03fh
Description of the data and file structure
Repository for the paper: “Asymmetry in cross-sex cross-trait genetic covariances and the evolvability of sexual dimorphism”
Authors & institutions:
Mathieu Videlier; mathieu.videlier@utoronto.ca
Jacqueline Sztepanacz; j.sztepanacz@utoronto.ca
Author affiliations: Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks street, Toronto, ON, M5S3B2, Canada
Responsible for collecting data: Mathieu Videlier
Responsible for writing code: Mathieu Videlier
Files and variables
File: data.zip
Description:
contains the following files:
- raw_data.csv: Dataset with information from literature survey
- combined_data.csv: Final dataset produced by running the script MAIN_SCRIPT_GMF_LIST.r
- VIDELIER_mvn_samples.csv : 1,000 REML-MVN samples of Gmf from Videlier, M., H. D. Rundle, and V. Careau. 2021. Sex‐specific genetic (co)variances of standard metabolic rate, body mass and locomotor activity in Drosophila melanogaster. Journal of Evolutionary Biology 34:1279–1289.
- SZTEPANACZ_mvn_samples.dat: 1,000 REML-MVN samples of Gmf from Sztepanacz, J. L., and D. Houle. 2019. Cross‐sex genetic covariances limit the evolvability of wing‐shape within and among species of Drosophila. Evolution 73:1617–1633.
- HOULE_mvn_samples.csv: 1,000 REML-MVN samples of Gmf from Houle, D., and C. Cheng. 2021. Predicting the Evolution of Sexual Dimorphism in Gene Expression. Molecular Biology and Evolution. 38:1847-1859
Description of datasets
Variables (columns) within data files:
folder “data”:
raw_data.csv:
[1] "Article.Nb": Unique numerical manuscript label
[2] "Article.Code" : Unique categorical (letter) manuscript label
[3] "Authors": First author of the manuscript
[4] "Year": Year of publication of the manuscript
[5] "NOTES": Notes associated with the manuscript. Empty cells in this column mean there are no notes associated with the study.
[6] "Journal": Name of the Journal publishing the manuscript
[7] "Title": Title of the manuscript
[8] "Gmf.dimension": Dimension of the Gmf
[9] "Traits": Traits of interest of the manuscript
[10] "Trait_Nature" : Category of the trait of interest
[11] "Species": Species of the system
[12] "Group": Category of the species
[13] "Laboratory...Field": Origin of the population of interest
[14] "Frequentist.Bayesien": Statistical category the original paper used for analysis (frequentist vs bayesian)
[15] "Genetic_Technics": Genetic technique used to obtain genetic variance
[16] "Stat_Methods": quantitative genetic model (sire, animal, parent-offspring regression, etc)
[17] "nb_ind" : number of individuals in the data
[18] "nb_fam": number of families in the data
[19] "Nature.variance": Additive or total genetic variance
[20] "Standardized.traits": Categorical variable indicating if variables are standardized
[21] "Standardized.Type": Technique used to standardize variable. Empty cells in this column mean the variables were not standardized.
[22] "UniqueTrait": Categorical variable indicating whether the traits are functionally related or not
[23] "Pronounced_SexualDimorphism": Categorical variable indicating if the traits have pronounced sexual dimorphism
[24] "Sexual.differential.trait..under.sexual.selection": Categorical variable indicating if the traits are usually under sexual selection
[25] "Test.B.0": Categorical variable indicating if the manuscript tests for B=0
[26] "Test.Asymmetry": Categorical variable indicating if the manuscript tests for B asymmetry.
combined_data.csv:
*NULL means the data was unavailable from the original study
*values of NA in this dataset indicates that the data required to produce these values were unavailable from the original study
[1] "PAPER": Unique manuscript label
[2] "SAMPLE": Unique numerical manuscript label
[3] "AUTHOR": First Author of the manuscript
[4] "YEAR": Year of publication of the manuscript
[5] "Gmf_Matrix": Gmf matrix
[6] "POP": Population label (if there is different Gmf)
[7] "CORRECTED": Factor variable indicating if Gmf corrected for negative eigenvalues (NearPD function)
[8] "TotVa_Gmf": Total genetic variance of Gmf
[9] "TotVa_Gf": Total genetic variance of Gf
[10] "TotVa_Gm": Total genetic variance of Gm
[11] "SDindex_TotVa": Sexual difference in total genetic variance from equation 1
[12] "TotVa_unshared": sexually-autonomous or unshared genetic variance (size of B matrix) from equation 2
[13] "Prop_TotVa_unshared": proportion of sexually-autonomous genetic variance
[14] "ND_Gmf": effective dimensionality of Gmf from equation 3
[15] "ND_Gf": effective dimensionality of Gf from equation 3
[16] "ND_Gm": effective dimensionality of Gm from equation 3
[17] "SDindex_ND": Sex difference in effective dimensionality
[18] "ND_DiffTotvsSex": Difference between the effective dimensionality of Gmf and the sum of the effective dimensionality of Gf and Gm
[19] "Sim_GfGm": Similarity between Gf and Gm from equation 4
[20] " Bm_norm": Frobenius norm of B
[21] "Prop_TotVa_shared": proportion of shared genetic variance
[22] "B_matrix": Between sex genetic variance
[23] "Asymetric_Prop": Asymmetry of the B matrix from equation 7
[24] "TotGenVar_Gmf": Total genetic variance of Gmf
[25] "GCA_Matrix": concordant-antagonistic genetic matrix from equation 6
[26] "TotGenVar_Gc": total genetic variance of Gc
[27] "TotGenVar_Ga": total genetic variance of Ga
[28] "PropGenVar_Gc": proportion of concordant genetic variance in GCA
[29] "PropGenVar_Ga": proportion of antagonistic genetic variance in GCA
[30] "size_Gc": Frobenius norm of Gc
[31] "size_Ga": Frobenius norm Ga
[32] "size_BCa": Frobenius norm Bca
[33] "Qac": ratio of Frobenius norm_Ga over Frobenius norm_Gc
[34] "Qind_c": log of the ratio of Frobenius norm_BCa over Frobenius norm_Gc
[35] "Qind_a": log of the ratio of Frobenius norm_BCa over Frobenius norm_Ga
[36] "Length_RSP_Zc_C": total length (Euclidean norm) of predicted responses to selection of Gc in sexual concordant scenario (mean)
[37] "Length_RSP_Zc_C_SEM": total length (Euclidean norm) of predicted responses to selection of Gc in sexual concordant scenario (mean standard error)
[38] "Length_RSP_Za_C": total length (Euclidean norm) of predicted responses to selection of Ga in sexual concordant scenario (mean)
[39] "Length_RSP_Za_C_SEM": total length (Euclidean norm) of predicted responses to selection of Ga in sexual concordant scenario (mean standard error)
[40] "Length_RSP_Zc_A": total length (Euclidean norm) of predicted responses to selection of Gc in sexual antagonist scenario (mean)
[41] "Length_RSP_Zc_A_SEM": total length (Euclidean norm) of predicted responses to selection of Gc in sexual antagonist scenario (mean standard error)
[42] "Length_RSP_Za_A": total length (Euclidean norm) of predicted responses to selection of Ga in sexual antagonist scenario (mean)
[43] "Length_RSP_Za_A_SEM": total length (Euclidean norm) predicted responses to selection of Ga in sexual antagonist scenario (mean standard error)
[44] "Rsp_C_indirect": ratio of RSP_Za_C over RSP_Zc_C (mean)
[45] "Rsp_C_indirect_SEM": ratio of RSP_Za_C over RSP_Zc_C (standard error of the mean)
[46] "Rsp_A_indirect": ratio of RSP_Zc_A over RSP_Za_A (mean)
[47] "Rsp_A_indirect_SEM": ratio of RSP_Zc_A over RSP_Za_A (standard error of the mean)
[48] "Rsp_C_indirect_log": log of Rsp_C_indirect (mean)
[49] "Rsp_C_indirect_log_SEM": log of Rsp_C_indirect (standard error of the mean)
[50] "Rsp_A_indirect_log": log of Rsp_A_indirect (mean)
[51] "Rsp_A_indirect_log_SEM": log of Rsp_A_indirect (standard error of the mean)
[52] "Init_C": projection of random sexually concordant selection gradient through observed Gmf (mean)
[53] "Init_C_SEM": projection of random sexually concordant selection gradient through observed Gmf (standard error of the mean)
[54] "NoAsym_C": projection of random sexually concordant selection gradient through Gmf B=symmetric (mean)
[55] "NoAsym_C_SEM": projection of random sexually concordant selection gradient through Gmf B=symmetric (standard error of the mean)
[56] "Diag_C": projection of random sexually concordant selection gradient through Gmf B=diagonal (mean)
[57] "Diag_C_SEM": tprojection of random sexually concordant selection gradient through Gmf B=diagonal (standard error of the mean)
[58] "B0_C": projection of random sexually concordant selection gradient through Gmf where B=0 (mean)
[59] "B0_C_SEM": projection of random sexually concordant selection gradient through Gmf where B=0 (standard error of the mean)
[60] "L_NoAsym_C": L ratio between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario (mean)
[61] "L_NoAsym_C_SEM": L ratio between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario(standard error of the mean)
[62] "L_Diag_C": L ratio between Gmf observed vs Gmf modified with B with just its diagonal for sexual concordant scenario (mean)
[63] "L_Diag_C_SEM": L ratio between Gmf observed vs Gmf modified with B with just its diagonal for sexual concordant scenario (standard error of the mean)
[64] "L_B0_C": L ratio between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (mean)
[65] "L_B0_C_SEM": L ratio between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[66] "L_NoAsymDiag_C": L ratio between Gmf modified with B symmetrical vs Gmf modified with B with just the diagonal for sexual concordant scenario (mean)
[67] "L_NoAsymDiag_C_SEM": L ratio between Gmf modified with B symmetrical vs Gmf modified with B with just the diagonal for sexual concordant scenario (standard error of the mean)
[68] "L_DiagB0_C": L ratio between Gmf modified with B with just the diagonal vs Gmf modified with B=0 for sexual concordant scenario (mean)
[69] "L_DiagB0_C_SEM": L ratio between Gmf modified with B with just the diagonal vs Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[70] "Prop_NoAsym_C": Part 1 of equation 8 for sexual concordant scenario (mean)
[71] "Prop_NoAsym_C_SEM": Part 1 of equation 8 for sexual concordant scenario (standard error of the mean)
[72] "Prop_NoAsymDiag_C": Part 2 of equation 8 for sexual concordant scenario (mean)
[73] "Prop_NoAsymDiag_C_SEM": Part 2 of equation 8 for sexual concordant scenario (standard error of the mean)
[74] "Prop_DiagB0_C": Part 3 of equation 8 for sexual concordant scenario (mean)
[75] "Prop_DiagB0_C_SE": Part 3 of equation 8 for sexual concordant scenario (standard error of the mean)
[76] "Init_A": projection of random sexually antagonistic selection gradient through observed Gmf (mean)
[77] "Init_A_SEM”: projection of random sexually antagonistic selection gradient through observed Gmf (standard error of the mean)
[78] "NoAsym_A": projection of random sexually antagonistic selection gradient through Gmf where B=symmetric (mean)
[79] "NoAsym_A_SEM": projection of random sexually antagonistic selection gradient through Gmf where B=symmetric (standard error of the mean)
[80] "Diag_A": tprojection of random sexually antagonistic selection gradient through Gmf where B=diagonal (mean)
[81] "Diag_A_SEM": projection of random sexually antagonistic selection gradient through Gmf where B=diagonal (standard error of the mean)
[82] "B0_A": projection of random sexually antagonistic selection gradient through Gmf where B=0 (mean)
[83] "B0_A_SE": projection of random sexually antagonistic selection gradient through Gmf where B=0 (standard error of the mean)
[84] "L_NoAsym_A": L ratio between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (mean)
[85] "L_NoAsym_A_SEM": ratio between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (standard error of the mean)
[86] "L_Diag_A": L ratio between Gmf observed vs Gmf modified with B with just its diagonal for sexual antagonistic scenario (mean)
[87] "L_Diag_A_SEM": L ratio between Gmf observed vs Gmf modified with B with just its diagonal for sexual antagonistic scenario (standard error of the mean)
[88] "L_B0_A": L ratio between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (mean)
[89] "L_B0_A_SEM": L ratio between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[90] "L_NoAsymDiag_A": L ratio between Gmf modified with B symmetrical vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (mean)
[91] "L_NoAsymDiag_A_SEM": L ratio between Gmf modified with B symmetrical vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (standard error of the mean)
[92] "L_DiagB0_A": L ratio between Gmf modified with B with just the diagonal vs Gmf modified with B=0 for sexual antagonistic scenario (mean)
[93] "L_DiagB0_A_SEM": L ratio between Gmf modified with B with just the diagonal vs Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[94] "Prop_NoAsym_A": Part 1 of equation 8 for sexual antagonistic scenario (mean)
[95] "Prop_NoAsym_A_SEM": Part 1 of equation 8 for sexual antagonistic scenario (standard error of the mean)
[96] "Prop_NoAsymDiag_A": Part 2 of equation 8 for sexual antagonistic scenario (mean)
[97] "Prop_NoAsymDiag_A_SEM": Part 2 of equation 8 for sexual antagonistic scenario (standard error of the mean)
[98] "Prop_DiagB0_A": Part 3 of equation 8 for sexual antagonistic scenario (mean)
[99] "Prop_DiagB0_A_SEM": Part 3 of equation 8 for sexual antagonistic scenario (standard error of the mean)
[100] "ANGLE_RxR_SYM_C": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario (mean)
[101] "ANGLE_RxR_SYM_C_SEM": Angle of the predicted concordant to selection between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario (standard error of the mean)
[102] "ANGLE_RxR_SYM_F_C": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario (mean)
[103] "ANGLE_RxR_SYM_F_C_SEM": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario (standard error of the mean)
[104] "ANGLE_RxR_SYM_M_C": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario (mean)
[105] "ANGLE_RxR_SYM_M_C_SEM": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual concordant scenario (standard error of the mean)
[106] "ANGLE_RxR_DIAG_C": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual concordant scenario (mean)
[107] "ANGLE_RxR_DIAG_C_SEM": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual concordant scenario (standard error of the mean)
[108] "ANGLE_RxR_DIAG_F_C": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual concordant scenario (mean)
[109] "ANGLE_RxR_DIAG_F_C_SEM": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual concordant scenario (standard error of the mean)
[110] "ANGLE_RxR_DIAG_M_C": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual concordant scenario (mean)
[111] "ANGLE_RxR_DIAG_M_C_SEM": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with just the B diagonal for sexual concordant scenario (standard error of the mean)
[112] "ANGLE_RxR_B0_C": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (mean)
[113] "ANGLE_RxR_B0_C_SEM": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[114] "ANGLE_RxR_B0_F_C": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (mean)
[115] "ANGLE_RxR_B0_F_C_SEM": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[116] "ANGLE_RxR_B0_M_C": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (mean)
[117] "ANGLE_RxR_B0_M_C_SEM": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[118] "ANGLE_BxR_INIT_C": Angle between selection gradient and predicted response to selection with Gmf observed for sexual concordant scenario (mean)
[119] "ANGLE_BxR_INIT_C_SEM": Angle between selection gradient and predicted response to selection with Gmf observed for sexual concordant scenario (standard error of the mean)
[120] "ANGLE_BxR_INIT_F_C": Female angle between selection gradient and predicted response to selection with Gmf observed for sexual concordant scenario (mean)
[121] "ANGLE_BxR_INIT_F_C_SEM": Female angle between selection gradient and predicted response to selection with Gmf observed for sexual concordant scenario (standard error of the mean)
[122] "ANGLE_BxR_INIT_M_C": Male angle between selection gradient and predicted response to selection with Gmf observed for sexual concordant scenario (mean)
[123] "ANGLE_BxR_INIT_M_C_SEM": Male angle between selection gradient and predicted response to selection with Gmf observed for sexual concordant scenario (standard error of the mean)
[124] "ANGLE_BxR_SYM_C": Angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual concordant scenario (mean)
[125] "ANGLE_BxR_SYM_C_SEM": Angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual concordant scenario (standard error of the mean)
[126] "ANGLE_BxR_SYM_F_C": Female angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual concordant scenario (mean)
[127] "ANGLE_BxR_SYM_F_C_SEM": Female angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual concordant scenario (standard error of the mean)
[128] "ANGLE_BxR_SYM_M_C": Male angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual concordant scenario (mean)
[129] "ANGLE_BxR_SYM_M_C_SEM": Male angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual concordant scenario (standard error of the mean)
[130] "ANGLE_BxR_DIAG_C": Angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual concordant scenario (mean)
[131] "ANGLE_BxR_DIAG_C_SEM": Angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual concordant scenario (standard error of the mean)
[132] "ANGLE_BxR_DIAG_F_C": Female angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual concordant scenario (mean)
[133] "ANGLE_BxR_DIAG_F_C_SEM": Female angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual concordant scenario (standard error of the mean)
[134] "ANGLE_BxR_DIAG_M_C": Male angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual concordant scenario (mean)
[135] "ANGLE_BxR_DIAG_M_C_SEM": Male angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual concordant scenario (standard error of the mean)
[136] "ANGLE_BxR_B0_C": Angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual concordant scenario (mean)
[137] "ANGLE_BxR_B0_C_SEM": Angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[138] "ANGLE_BxR_B0_F_C": Female angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual concordant scenario (mean)
[139] "ANGLE_BxR_B0_F_C_SEM": Female angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[140] "ANGLE_BxR_B0_M_C": Male angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual concordant scenario (mean)
[141] "ANGLE_BxR_B0_M_C_SEM": Male angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual concordant scenario (standard error of the mean)
[142] "ANGLE_RxR_SYM_A": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (mean)
[143] "ANGLE_RxR_SYM_A_SEM": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (standard error of the mean)
[144] "ANGLE_RxR_SYM_F_A": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (mean)
[145] "ANGLE_RxR_SYM_F_A_SEM": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (standard error of the mean)
[146] "ANGLE_RxR_SYM_M_A": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (mean)
[147] "ANGLE_RxR_SYM_M_A_SEM": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B symmetrical for sexual antagonistic scenario (standard error of the mean)
[148] "ANGLE_RxR_DIAG_A": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (mean)
[149] "ANGLE_RxR_DIAG_A_SEM": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (standard error of the mean)
[150] "ANGLE_RxR_DIAG_F_A": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (mean)
[151] "ANGLE_RxR_DIAG_F_A_SEM": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (standard error of the mean)
[152] "ANGLE_RxR_DIAG_M_A": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (mean)
[153] "ANGLE_RxR_DIAG_M_A_SEM": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B with just the diagonal for sexual antagonistic scenario (standard error of the mean)
[154] "ANGLE_RxR_B0_A": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (mean)
[155] "ANGLE_RxR_B0_A_SEM": Angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[156] "ANGLE_RxR_B0_F_A": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (mean)
[157] "ANGLE_RxR_B0_F_A_SEM": Female angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[158] "ANGLE_RxR_B0_M_A": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (mean)
[159] "ANGLE_RxR_B0_M_A_SEM": Male angle of the predicted response to selection between Gmf observed vs Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[160] "ANGLE_BxR_INIT_A": Angle between selection gradient and predicted response to selection with Gmf observed for sexual antagonistic scenario (mean)
[161] "ANGLE_BxR_INIT_A_SEM": Angle between selection gradient and predicted response to selection with Gmf observed for sexual antagonistic scenario (standard error of the mean)
[162] "ANGLE_BxR_INIT_F_A": Female angle between selection gradient and predicted response to selection with Gmf observed for sexual antagonistic scenario (mean)
[163] "ANGLE_BxR_INIT_F_A_SEM": Female angle between selection gradient and predicted response to selection with Gmf observed for sexual antagonistic scenario (standard error of the mean)
[164] "ANGLE_BxR_INIT_M_A": Male angle between selection gradient and predicted response to selection with Gmf observed for sexual antagonistic scenario (mean)
[165] "ANGLE_BxR_INIT_M_A_SEM": Male angle between selection gradient and predicted response to selection with Gmf observed for sexual antagonistic scenario (standard error of the mean)
[166] "ANGLE_BxR_SYM_A": Angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual antagonistic scenario (mean)
[167] "ANGLE_BxR_SYM_A_SEM": Angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual antagonistic scenario (standard error of the mean)
[168] "ANGLE_BxR_SYM_F_A": Female angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual antagonistic scenario (mean)
[169] "ANGLE_BxR_SYM_F_A_SEM": Female angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual antagonistic scenario (standard error of the mean)
[170] "ANGLE_BxR_SYM_M_A": Male angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual antagonistic scenario (mean)
[171] "ANGLE_BxR_SYM_M_A_SEM" Male angle between selection gradient and predicted response to selection with Gmf modified with B symmetrical for sexual antagonistic scenario (standard error of the mean)
[172] "ANGLE_BxR_DIAG_A": Angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual antagonistic scenario (mean)
[173] "ANGLE_BxR_DIAG_A_SEM": Angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual antagonistic scenario (standard error of the mean)
[174] "ANGLE_BxR_DIAG_F_A": Female angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual antagonistic scenario (mean)
[175] "ANGLE_BxR_DIAG_F_A_SEM": Female angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual antagonistic scenario (standard error of the mean)
[176] "ANGLE_BxR_DIAG_M_A": Male angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual antagonistic scenario (mean)
[177] "ANGLE_BxR_DIAG_M_A_SEM": Male angle between selection gradient and predicted response to selection with Gmf modified with B with just the diagonal for sexual antagonistic scenario (standard error of the mean)
[178] "ANGLE_BxR_B0_A": Angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual antagonistic scenario (mean)
[179] "ANGLE_BxR_B0_A_SEM": Angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[180] "ANGLE_BxR_B0_F_A": Female angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual antagonistic scenario (mean)
[181] "ANGLE_BxR_B0_F_A_SEM": Female angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[182] "ANGLE_BxR_B0_M_A": Male angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual antagonistic scenario (mean)
[183] "ANGLE_BxR_B0_M_A_SEM": Male angle between selection gradient and predicted response to selection with Gmf modified with B=0 for sexual antagonistic scenario (standard error of the mean)
[184] "Article.Nb": Unique numerical manuscript label
[185] "Article.Code": Unique categorical (letter) manuscript label
[186] "Authors": First author of the manuscript
[187] "Year": Year of publication of the manuscript
[188] "NOTES": Notes associated to the manuscript
[189] "Journal": Name of the Journal publishing the manuscript
[190] "Title": Title of the manuscript
[191] "Gmf.dimension": Dimension of the Gmf
[192] "Traits": Traits of interest of the manuscript
[193] "Trait_Nature": Category of the trait of interest
[194] "Species": Species of the system
[195] "Group": Group species of the system
[196] "Laboratory...Field": Origin of the population of interest
[197] "Frequentist.Bayesien": Statistical category use for analysis in the original paper (frequentist vs bayesian)
[198] "Genetic_Technics": Genetic technique used to obtain genetic variance
[199] "Stat_Methods": Statistical methods
[200] "nb_ind": number of individuals in the data
[201] "nb_fam": number of family in the data
[202] "Nature.variance": Additive or total genetic variance
[203] "Standardized.traits": Categorical variable indicating if variables are standardized
[204] "Standardized.Type": Technique used to standardize variable
[205] "UniqueTrait": Categorical variable indicating whether the traits are functionally related or not
[206] "Pronounced_SexualDimorphism": Categorical variable indicating if the traits have pronounced sexual dimorphism
[207] "Sexual.differential.trait.under.sexual.selection": Categorical variable indicating if the traits are usually under sexual selection
[208] "Test.B.0": Categorical variable indicating if the manuscript tests for B=0
[209] "Test.Asymmetry": Categorical variable indicating if the manuscript tests for B asymmetry
[210] "Matrix.Code" : Label for each manuscript for figure
Code/software
Software version and package information
- R version 4.4.2 (2024-10-31 ucrt)
- Platform: x86_64-w64-mingw32/x64
- Running under: Windows 11 x64 (build 26100)
R-packages:
attached base packages:
stats, graphics, grDevices, utils, datasets, methods, base
other attached packages:
PerformanceAnalytics_2.0.8
xts_0.14.1
zoo_1.8-12
data.table_1.16.2
beepr_2.0
evolvability_2.0.0
Matrix_1.7-1
moments_0.14.1
loaded via a namespace (and not attached):
lme4_1.1-35.5
digest_0.6.37
lattice_0.22-6
splines_4.4.2
audio_0.1-11
parallel_4.4.2
ape_5.8-1
nloptr_2.1.1
grid_4.4.2
compiler_4.4.2
boot_1.3-31
nlme_3.1-166
minqa_1.2.8
Rcpp_1.0.13-1
quadprog_1.5-8
MASS_7.3-61
“scripts” contains the following files:
MAIN_SCRIPT_GMF_LIST.r: run this script first to generate the file “combined_data.csv”
MANUSCRIPT_RESULT.r: run this script second to generate the main results that are shown in the manuscript
MANUSCRIPT_GRAPH.r: run this script third to generate Figs1 - S6b
MV_RandomSampling_GMF.r: run this script to generate the mean with CI of columns in combined_data.csv for the 1,000 REML-MVN samples of “VIDELIER_mvn_samples.csv “, “SZTEPANACZ_mvn_samples.dat”, and “HOULE_mvn_samples.csv”. Due to the long computational time , intermediate output files have been saved in the folder “../results/random_sampling_intermediate_files”.
MV_RandomSampling_Gmf_Graph.r: run this script to generate FigsS7 - S12
subfolder: “source files” contains R scripts that are called by MAIN_SCRIPT_GMF_LIST.r and by MV_RandomSampling_GMF.r. Do not run these scripts independently
-Analysis_Part_1.r: Script to produce the dataset structure, load packages and call for local functions
-Analysis_Part_2.r: Script to extract all the information from Gmf, as well to produce random skewers (selection gradients), L ratio, and angles.
-Analysis_Part_3.r: Script to combine the final dataset and the literature review files (“raw_data.csv”) to produce the final file (“combined_data.csv”).
-Analysis_Part1_RS.r: Script to produce the dataset structure and call for functions
-Analysis_Part2_RS.r: Script to extract all the information from resampling Gmf matrices, as well to produce random skewers (selection gradients), L ratio, and angles.
“results” contains the results of the analyses:
subfolder “figures” contains all figures shown in the manuscript ie) Figs1 - S6b generated by MANUSCRIPT_GRAPH.r
subfolder “random_sampling_intermediate_files” contains files produced by MV_RandomSampling_GMF.r.
subfolder “random_sampling_figures” contains FigsS7 - S12 generated by MV_RandomSampling_Gmf_Graph.r
subfolder: “Random_sampling_intermediate_files”
All files follow the same structure as “combined_data” with mean and CI (quantile 2.5% and 95.7%) for each Gmf (Houle, Videlier, Sztepanacz)
- BETA_VIDELIER.csv: Storage selection gradients from the Analysis_Part_2 for VIDELIER Gmf
- ASYM_VIDELIER_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of Gmf resampling of VIDELIER metric
- RSP_Gca_VIDELIER_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of respondability of concordant -antagonistic genetic matrix of SZTEPANACZ resampling
- Angle_VIDELIER_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of angle of VIDELIER Gmf resampling
- Lmetric_VIDELIER_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of L ratio of VIDELIER Gmf resampling
- BETA_SZTEPANACZ.csv: Storage selection gradients from the Analysis_Part_2 for SZTEPANACZ Gmf
- ASYM_SZTEPANACZ_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of Gmf resampling of SZTEPANACZ metric
- RSP_Gca_SZTEPANACZ_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of respondability of concordant -antagonistic genetic matrix of SZTEPANACZ resampling
- Angle_SZTEPANACZ_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of angle of SZTEPANACZ Gmf resampling
- Lmetric_SZTEPANACZ_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of L ratio of SZTEPANACZ Gmf resampling
- BETA_HOULE.csv: Storage selection gradients from the Analysis_Part_2 for HOULE Gmf
- ASYM_HOULE_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of Gmf resampling of HOULE metric
- RSP_Gca_HOULE_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of respondability of concordant -antagonistic genetic matrix of HOULE resampling
- Angle_HOULE_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of angle of HOULE Gmf resampling
- Lmetric_HOULE_MEANCI.csv : mean and confidence interval (quantile 2.5 and 97.5) of L ratio of HOULE Gmf resampling
