Supplemental Material for Jue et al., 2018

Figure S1 - Intact ovary removed from gravid female.

Figure S2 - Species tree used in PAML.

Figure S3 - Average expression in fragments per kilobase per million base pairs (FPKM) in each tissue grouped by cluster genes indicating which clusters are associated with which tissues.

Figure S4 - Level 2 Biological Process and Molecular Function Gene Ontology terms associated with gene identified as having sites under positive selection in Poeciliids.

Figure S5 - Phylogenetic distance-based gene-family tree for RAB11 family-interacting proteins (RAB11FIPs) in fishes.

Table S1. Detail of Each Read Libraries

Table S2. Number of predicted transcripts in each coverage bin from SwissProt reference mapping

Table S3. Repetitive elements in reference transcriptome with associated gene expression in placental and embryonic tissues. From the total transcriptome, 26,102 transcripts had low sequence complexity or simple repeats, 13,083 transcripts shared homology with either DNA transposons or retroelements from REPBASE database, and 1,442 transcripts showing evidence of both. A further 8,182 transcripts could be associateds with repetitive elements from nt reference sequences.

Table S4. Counts of known non-coding RNAs identified by homolog in Poeciliopsis prolifica

Table S5. Number of transcripts with frameshifts or ambiguous bases in transcriptome sequence for each species listed

Table S6. Summary of ORFs and site under positive selection from PAML analysis.

Table S7. Combined results of PAML analysis. Table displays annotations, identities and number of sites identified as a being under positive selection for all coding sequences identified to be rapidly evolving.

Table S8. Combined results of PAML analysis for sites in genes under positive selection shared for "Xiphophorus/lecithotroph" and "Poeciliid/live-bearer" foreground tests for positive selection. Table displays annotations, identities and number of sites identified as a being under positive selection in coding sequences identified to be rapidly evolving under aforementioned analysis conditions.

Table S9. Results of PAML analysis for sites in genes under positive selection for "Xiphophorus/lecithotroph" only foreground tests for positive selection. Table displays annotations, identities and number of sites identified as a being under positive selection in coding sequences identified to be rapidly evolving under aforementioned analysis conditions.

Table S10. Combined results of PAML analysis for sites in genes under positive selection shared for "Poeciliopsis/matrotroph" and "Poeciliid/live-bearer" foreground tests for positive selection. Table displays annotations, identities and number of sites identified as a being under positive selection in coding sequences identified to be rapidly evolving under aforementioned analysis conditions.

Table S11. Results of PAML analysis for sites in genes under positive selection for "Poeciliopsis/matrotroph" only foreground tests for positive selection. Table displays annotations, identities and number of sites identified as a being under positive selection in coding sequences identified to be rapidly evolving under aforementioned analysis conditions.

Table S12. Results of PAML analysis for sites in genes under positive selection for "Poeciliids/live-bearers" only foreground tests for positive selection. Table displays annotations, identities and number of sites identified as a being under positive selection in coding sequences identified to be rapidly evolving under aforementioned analysis conditions.

Table S13. Results of PAML analysis for sites in genes under positive selection in all foreground tests for positive selection. Table displays annotations, identities and number of sites identified as a being under positive selection in coding sequences identified to be rapidly evolving under aforementioned analysis conditions.