DOI: 10.25338/b8gc91
title: Correlated evolution of sex allocation and mating system in wrasses and parrotfishes

description: In accordance with predictions of the size-advantage model, comparative
 evidence confirms that protogynous sex change is lost when mating behavior
 is characterized by weak size advantage. However, we lack comparative
 evidence supporting the adaptive significance of sex change. Specifically,
 it remains unclear whether increasing male size advantage induces
 transitions to protogynous sex change across species, as it can within
 species. We show that in wrasses and parrotfishes (Labridae), the
 evolution of protogynous sex change is correlated with polygynous mating,
 and that the degree of male size advantage expressed by polygynous species
 influences transitions between different types of protogynous sex change.
 Phylogenetic reconstructions reveal strikingly similar patterns of sex
 allocation and mating system evolution with comparable lability. Despite
 the plasticity of sex determination mechanisms in labrids, transitions
 trend towards monandry (all males derived from sex-changed females), with
 all observed losses of protogyny accounted for by shifts in the timing of
 sex change to prematuration. Likewise, transitions in mating system trend
 from the ancestral condition of lek-like polygyny toward greater male size
 advantage, characteristic of haremic polygyny. The results of our
 comparative analyses are among the first to confirm the adaptive
 significance of sex change as described by the size-advantage model.
description: <strong>Trait data compilation</strong>
 Data on species-specific mating systems and sex allocation
 pathways were compilied from the primary literature (file:
 <strong>TableS5.xlsx</strong>, references are listed
 within). The types of sex allocation and mating systems expressed by
 labrid fishes, their definitions and predicted associations with the
 degree of male size advantage are detailed in figure 1. Mating system
 classifications focused only on terminal phase males and did not consider
 the mating strategies of initial phase males – although it is known that
 the reproductive output of initial phase males can outweigh that of
 terminal phase males for some species dependent on location-specific
 population dynamics (Warner and Hoffman
 1980<i>a</i>,<i>b</i>; Warner 1982). We applied
 the consensus classification of the predominant mating system (i.e.
 supported by multiple authors) whenever possible, and otherwise relied on
 the most recent observations. We restricted sexual ontogeny data to
 accounts of protogyny that were distinguishable as either monandric or
 diandric based on gonad histology, population demographics or both. Cases
 where males are derived from females that have not passed through a
 functional stage were categorized as functionally gonochoristic following
 previous work (Sadovy and Shapiro 1987; Sadovy de Mitcheson and Liu 2008;
 Kazancıoğlu and Alonzo 2010; Erisman et al. 2013). Mating system and
 sex-change data were available for 89 labrid species. 
 <b>Phylogenetic inference and divergence time
 estimation</b> Gene sequences were
 aligned separately in Geneious Pro R8.1.9 (http://www.geneious.com/) using
 default settings and the alignments were manually adjusted through the
 insertion or deletion of gaps and trimmed to minimize the amount of
 missing data. Alignments were concatenated and partitioned by gene region,
 with separate partitions for the 3<sup>rd</sup> codon position
 of protein coding genes.
 Bayesian inference (BI) using partitioned mixed
 models in MrBayes v3.2.3 (Ronquist and Huelsenbeck 2003) was implemented
 on the CIPRES Science Gateway portal (Miller et al. 2010) to estimate the
 tree topology and branch lengths. We sampled across the entire general
 time reversible (GTR) model space using reversible jump Markov chain Monte
 Carlo (rjMCMC) methods to integrate out uncertainty about the correct
 substitution model for each partition (nst = mixed). This allowed us to
 quantify posterior probabilities of the substitution models sampled (i.e.
 the probability of each substitution model conditional on the data; table
 S3). Parameters were unlinked across partitions. Substitution rates and
 stationary nucleotide frequencies were allowed to evolve under different
 rates using a flat Dirichlet prior. The shape of the gamma distribution of
 rate variation evolved under an exponential prior with a mean of one.
 Branch lengths were unconstrained under an exponential prior with a rate
 of 200 (mean = 0.005). Posterior probabilities of clades were calculated
 following two 40 million generation Markov chain Monte Carlo (MCMC)
 analyses, each with eight chains (temp = 0.02) and two swaps, sampling
 every 2,000 generations. Convergence was assessed in Tracer v1.5 (Rambaut
 et al. 2009). Upon examination of the trace files, a conservative burn-in
 of 45% was discarded from each run and a 50% majority-rule consensus tree
 was computed using the remaining sampled trees (file:
 <strong>MrBayes_ConsensusTree.nex</strong>). To estimate the temporal component of evolution, we first converted the majority-rule consensus tree to a rooted, ultrametric tree using the chronos function in the R package ape v3.2 (Paradis et al. 2004). We set the smoothing parameter lambda to 0.9 and specified a relaxed model of substitution rate variation among branches and seven age constraints (table S4). We then performed a divergence time analysis in BEAST v1.8.1 (Drummond et al. 2012) using the resultant ultrametric tree as the starting tree. Partitioning followed the scheme above and models of molecular evolution were specified using the parameters and priors corresponding to the model with the highest posterior probability from the MrBayes analysis and empirical base frequencies (see table S3 for substitution model details). Divergence times were estimated under a relaxed uncorrelated lognormal clock model (Drummond et al. 2006) and the birth-death process (Gernhard 2008). Evidence from six fossils informed exponential priors on corresponding nodes (table S4) to time-calibrate the trees. Exponential priors were used because they include the minimum age of the fossil and accommodate uncertainty in the age of the clade relative to the age of the fossil with soft upper-bounds. Monophyly of the Labridae was enforced based on previous phylogenetic reconstructions (Westneat and Alfaro 2005; Alfaro et al. 2009; Cowman and Bellwood 2011; Baliga and Law 2016). Posterior samples from three independent MCMC analyses, each with 80 million generations, sampling every 4,000 generations, were assessed for convergence and appropriate burn-in in Tracer v1.5 (Rambaut et al. 2009). Tree files were combined using LogCombiner v1.8.1 (Drummond et al. 2012) following the removal of 27.5–40% burn-in, and resampling every 16,000 states (file: <strong>PosteriorDistribution_9625TimeTrees.trees</strong>). A maximum clade credibility tree was constructed using TreeAnnotator v1.8.1 (Drummond et al. 2012) to display median ages and 95% highest posterior density (HPD) intervals (fig. S1; file: <strong>MaximumCladeCredibility_TimeTree.nex</strong>).  We randomly sampled 1,000 time-calibrated phylogenies from the posterior distribution and pruned them to match our trait dataset (n = 89 species; file: <strong>RandomSample_1000TimeTrees_89spp.nex</strong>). Further pruning was required for the second trait correlation analysis we ran in Discrete to assess predicted correlations between polygyny and protogyny with different degrees of male size advantage (species coded as either lek-like of haremic and diandric or monandric; n = 70 species; file: <strong>RandomSample_1000TimeTrees_70spp.nex</strong>).
description: <strong>TableS5.xlsx</strong>
 Mating system or sex allocation data are available for other
 labrid species. We considered only those species with both types of data
 avialable that met our source requirements.