Multiple evolutionary transitions of reproductive strategies in a phylum of aquatic colonial invertebrates

<strong>PHYLOGENIES</strong> <strong>All_genes_alignment.nex</strong> The concatenated mixed alignment consisting of, 13 mitochondrial protein-coding genes as amino acids, mitochondrial ribosomal RNA genes 12S+16S, and nuclear 18S+28S rRNA genes. Gene boundaries and excludes sites are indicated. <strong>Fig_2.nex</strong> Topology of the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in MrBayes5D v. 3.2.6 under the GTR+G model of nucleotide evolution (nucleotides) and the MTZOA+G model (amino acids). The analysis was run for 2.4 million generations; 1.5 million generations were discarded as burn-in. <strong>Fig_S3</strong> Topology of the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes (PCGs) as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in p4 under the GTR+G model of nucleotide evolution (nucleotides) and the MTZOA+G+F model (amino acids). The +F model component accommodates empirical composition in the amino acid model. The analysis used three separate runs for 300,000 generations; 200,000 generations were discarded as burn-in. <strong>Fig_S4</strong> Topology of the maximum likelihood phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the GTR+G (nucleotides) and the MTZOA+G+F models (amino acids). <strong>Fig_S5</strong> Topology of the Bayesian phylogenetic analysis of the 12S+16S rRNA gene partition constructed using MrBayes v. 3.2.6 under the GTR + G model. The analysis was run for 20 million generations; 10 million generations were discarded as burn-in. <strong>Fig_S6</strong> Topology of the maximum likelihood phylogenetic analysis of the 12S+16S rRNA gene partition constructed using RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the GTRCAT model. <strong>Fig_S7</strong> Topology of the Bayesian phylogenetic analysis of the 18S+28S rRNA gene partition constructed using MrBayes v. 3.2.6 under the GTR + G model. The analysis was run for 20 million generations; 10 million generations were discarded as burn-in. <strong>Fig_S8</strong> Topology of the maximum likelihood phylogenetic analysis of the 18S+28S rRNA gene partition constructed using RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the GTRCAT model. <strong>Fig_S9</strong> Topology of the Bayesian phylogenetic analysis of 13 mitochondrial protein-coding genes as amino acids constructed using MrBayes5D v. 3.2.6 under the MTZOA+G model. The analysis was run for 3.7 million generations; 2.5 million generations were discarded as burn-in. <strong>Fig_S10</strong> Topology of the maximum likelihood phylogenetic analysis of 13 mitochondrial protein-coding genes as amino acids constructed using RAxML HPC-PTHREADS-SSE3 v. 8.2.12 under the PROTGAMMAMTZOA model. <strong>Fig_S11</strong> Topology of the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions: (i) 13 mitochondrial protein-coding genes (PCGs) as amino acids, (ii) mitochondrial ribosomal RNA genes 12S+16S, (iii) nuclear 18S+28S rRNA genes. The analysis was performed in p4 under the NDCH-C2 model. The analysis used four separate runs for 300,000 generations; 200,000 generations were discarded as burn-in. The NDCH model accommodates compositional tree-heterogeneity and was used because there was a large amount of compositional heterogeneity over the sequences, especially in the PCGs and 12S+16S rRNA data partitions. This is an NDCH model with two composition vectors on each of the three data partitions. <strong>ANCESTRAL CHARACTER ESTIMATION:</strong> <strong>ACE.R</strong> R script of the ancestral character estimation carried out in phytools. <strong>Reproductive_strategy_numbers.csv</strong> Data input file for ACE analysis (reproductive strategies coded as numbers) <strong>Reproductive_strategies.xlsx</strong> List of reproductive strategies per taxon with the corresponding numerical codes used in the file 'Reproductive_stategies_numbers.csv'. <strong>Tree.tre</strong> Input tree for ACE analysis.