Computational protocol: Biomechanical Diversity of Mating Structures among Harvestmen Species Is Consistent with a Spectrum of Precopulatory Strategies

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Protocol publication

[…] Species means were compiled and imported into the R software environment []. We estimated phylogenetic signal in the data using Pagel's lambda [,] calculated in the geiger package []. Although lambda was found to be very low for all variables, we used appropriate comparative tests to compensate for any residual phylogenetic signal.We regarded a significant positive correlation between male and female variables as corroborating the prediction of sexual coevolution. We assessed the intersexual correlation using all variables simultaneously by phylogenetic canonical correlation analysis (pCCA) [,] with variables categorized by sex. We also conducted bivariate phylogenetic regressions analyses (pRA) [] between all pairs of male and female variables.The hypothesis that solicitous courtship and precopulatory antagonism operate in a mutually exclusive manner predicts that species should be distributed in two distinct clusters. The prediction was assessed using several methods. Cluster analysis was performed using a model-based approach [] implemented in mclust [], which evaluates results from different clustering models using the Bayesian Information Criterion (BIC). Recovery of two unmixed clusters would corroborate the distinctiveness of solicitous courtship and precopulatory antagonism. We also assessed whether interspecific variation was distributed continuously or clustered into functional groups by examining species scores from the pCCA, pRAs and pPCA [], although these methods are not optimized for group classification [].We tested the prediction that species with penile sacs and unarmed female genital opercula occupy a distinct solicitous group, and that those without penile sacs but with female pregenital armature occupy a distinct antagonistic category. We used phylogenetic flexible discriminant analysis [] and standard (non-phylogenetic) linear discriminant analysis in the MASS package [] for one set of analyses using presence or absence of penile gift-bearing sacs as the grouping variable and another set of analyses using presence or absence of female pregenital barriers. […]

Pipeline specifications

Software tools GEIGER, mclust
Application Phylogenetics