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

PHYLOGENIES

All_genes_alignment.nex

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.

Fig_2.nex

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.

Fig_S3

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.

Fig_S4

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).

Fig_S5

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.

Fig_S6

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.

Fig_S7

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.

Fig_S8

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.

Fig_S9

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.

Fig_S10

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.

Fig_S11

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.

Fig_S12

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. This analysis excluded all terminals for which less than half of mitogenome genes were available, or which only had one of the two nuclear 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 350,000 generations; 125,000 generations were discarded as burn-in.

Fig_S13

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. This analysis excluded all terminals for which less than half of mitogenome genes were available, or which only had one of the two nuclear 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).

ANCESTRAL CHARACTER ESTIMATION:

ACE.R

R script of the ancestral character estimation carried out in phytools.

Reproductive_strategy_numbers.csv

Data input file for ACE analysis (reproductive strategies coded as numbers)

Reproductive_strategies.xlsx

List of reproductive strategies per taxon with the corresponding numerical codes used in the file 'Reproductive_stategies_numbers.csv'.

Tree.tre

Input tree for ACE analysis.