Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals

Supplementary Material for:

Emerling C.A., Springer M.S., Gatesy J., Jones Z., Hamilton D., Xia-Zhu D., Collin M.A., and Delsuc F. (2021). Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals. Open Research Europe.

Supplementary File Legends:

- Supplementary_Figure_S1.pdf: RAxML AANAT gene tree.

- Supplementary_Figure_S2.pdf: RAxML ASMT gene tree.

- Supplementary_Figure_S3.pdf: RAxML MTNR1A+MTNR1B tree.

- Supplementary_Figure_S4.pdf: PAML AANAT results, model 1 (see Supplementary Table S7).

- Supplementary_Figure_S5.pdf: PAML ASMT results, model 2 (see Supplementary Table S8).

- Supplementary_Figure_S6.pdf: PAML MTNR1A results, model 1 (see Supplementary Table S9).

- Supplementary_Figure_S7.pdf: PAML MTNR1B results, model 1 (see Supplementary Table S10).

- Supplementary_Table_S1.xlsx: List of species examined in this study and the sources of the genes. Source key: WGS: Sequences derived from NCBI's Whole Genome Shotgun database; Whole Genome Sequencing of Short Reads: whole genomes were sequenced using short-read technologies. The methodologies  varied for the species, and will be published with other projects, so please contact the author(s) for information on the specific methodology and samples used; SRA: sequences derived from NCBI's Sequence Read Archive; GenBank: sequences derived from NCBI's nucleotide collection; Bowhead Whale Genome Resource: sequences derived from http://www.bowhead-whale.org; Ensembl: sequences derived from Ensembl genome browser (www.ensembl.org)l; Discovar de novo: sequences derived genomes assembled via Discovar de novo  (https://software.broadinstitute.org/software/discovar/blog/).

- Supplementary_Table_S2.xlsx: Accession numbers and functionality of AANAT in species examined. Parentheses after accession number indicates coordinates for sequence on the contig / scaffold. Exon colors code for the following: green = putatively functional; yellow = missing; pink = one or more inactivating mutations found. Abbreviations for mutations are as follows: del = deletion; ins = insertion; start = start codon mutation; stop = premature stop codon; ? = ambiguity whether the mutation is shared among all members of the clade. Abbreviations in brackets following an inactivating mutation indicate shared inactivating mutation. Key for each abbreviation follows: Bacu = Balaenoptera acutorostrata; BALA = Balaenidae; BALAEN = Balaenopteridae; Bbon = Balaenoptera bonaerensis; CAB = Cabassous; Ccap = Cebus capucinus; CETA = Cetacea; CHLAM = Chlamyphoridae; CHOL = Choloepus; Cjac = Callithrix jacchus; CING = Cingulata; DASY = Dasypodidae; DELP = Delphinidae; DERM = Dermoptera; Erob = Eschrichtius robustus; INIA = Inia; FOLI = Folivora; GALE = Galeopterus; LIPO = Lipotes; Lobl = Lagenorhynchus obliquidens; MANI = Manidae; MONO = Monodontidae; MYRM = Myrmecophagidae; MYST = Mysticeti; NPP = Not present in Platanista or Physeteroidea, but present in other Odontocetes; NPZ = Not present in Ziphiidae, but present in other Odontocetes; Oorc = Orcinus orca; PEUT = Tolypeutinae; PHOC = Phocoenidae; PHOL = Pholidota; PHOR = Chlamyphorinae; PILO = Pilosa; PHYS = Physeteroidea; PONT = Pontoporia; Schi = Sousa chinensis; SIRE = Sirenia; Tadu = Tursiops aduncus; TOLY = Tolypeutes; VERM = Vermilingua; XEN = Xenarthra.

- Supplementary_Table_S3.xlsx: Accession numbers and functionality of ASMT in species examined. See Table S2 caption for details.

- Supplementary_Table_S4.xlsx: Accession numbers and functionality of MTNR1A in species examined. See Table S2 caption for details.

- Supplementary_Table_S5.xlsx: Accession numbers and functionality of MTNR1B in species examined. See Table S2 caption for details.

- Supplementary_Table_S6.xlsx: Codon frequency model selection. These are the results from one ratio dN/dS analyses using different codon frequency models. 

- Supplementary_Table_S7.xlsx: Results of AANAT PAML dN/dS analyses. Model: BG = branch(es) grouped with background; fixed 1 = branch(es) fixed at 1. p-value: specific p-value only shown if lower than 0.05. Model Comparison: if model comparison yields statistically significant differences (p < 0.05), model comparison bolded and given green background. For most models, w only shown for branch(es) of interest.

- Supplementary_Table_S8.xlsx: Results of ASMT PAML dN/dS analyses. Refer to Table S7 caption for additional details.

- Supplementary_Table_S9.xlsx: Results of MTNR1A PAML dN/dS analyses. Refer to Table S7 caption for additional details.

- Supplementary_Table_S10.xlsx: Results of MTNR1B PAML dN/dS analyses. Refer to Table S7 caption for additional details.

- Supplementary_Table_S11.xlsx: Results of BLASTing and mapping short reads from Alligator mississippiensis RNA sequencing experiments.

- Supplementary_Dataset_S1_all_ali_fasta.txt: Genomic alignments in fasta format used to determine the pseudogene/functional status of the different genes in different taxonomic groups.

- Supplementary_Dataset_S2_AANAT_RAxML_ali.phy: Alignment of AANAT in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. 

- Supplementary_Dataset_S3_ASMT_RAxML_ali.phy: Alignment of ASMT in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. 

- Supplementary_Dataset_S4_MTNR1A_MTNR1B_RAxML_ali.phy: Alignment of MTNR1A and MTNR1B in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. 

- Supplementary_Dataset_S5_AANAT_PAML_alig.fasta: Codon alignment of AANAT in fasta format used in selection pressure analyses with PAML. 

- Supplementary_Dataset_S6_ASMT_PAML_ali.fasta: Codon alignment of ASMT in fasta format used in selection pressure analyses with PAML.

- Supplementary_Dataset_S7_MTNR1A_PAML_ali.fasta: Codon alignment of MTNR1A in fasta format used in selection pressure analyses with PAML.

- Supplementary_Dataset_S8_MTNR1B_PAML_ali.fasta: Codon alignment of MTNR1B in fasta format used in selection pressure analyses with PAML.

- Supplementary_Dataset_S9_PAML_topology.tre: Tree topology in newick format used in selection pressure analyses with PAML.