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.

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.