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

<strong>Supplementary Material for:</strong> 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.<strong><em> Open Research Europe.</em></strong> <strong>Supplementary File Legends:</strong> <strong>- Supplementary_Figure_S1.pdf:</strong> RAxML AANAT gene tree. <strong>- Supplementary_Figure_S2.pdf: </strong>RAxML ASMT gene tree. <strong>- Supplementary_Figure_S3.pdf: </strong>RAxML MTNR1A+MTNR1B tree. <strong>- Supplementary_Figure_S4.pdf: </strong>PAML AANAT results, model 1 (see Supplementary Table S7). <strong>- Supplementary_Figure_S5.pdf: </strong>PAML ASMT results, model 2<strong> </strong>(see Supplementary Table S8). <strong>- Supplementary_Figure_S6.pdf: </strong>PAML MTNR1A results, model 1 (see Supplementary Table S9). <strong>- Supplementary_Figure_S7.pdf: </strong>PAML MTNR1B results, model 1 (see Supplementary Table S10). <strong>- Supplementary_Table_S1.xlsx: </strong>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/). <strong>- Supplementary_Table_S2.xlsx: </strong>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 = <em>Balaenoptera acutorostrata</em>; BALA = Balaenidae; BALAEN = Balaenopteridae; Bbon = <em>Balaenoptera bonaerensis</em>; CAB = <em>Cabassous</em>; Ccap = <em>Cebus capucinus</em>; CETA = Cetacea; CHLAM = Chlamyphoridae; CHOL = <em>Choloepus</em>; Cjac = <em>Callithrix jacchus</em>; CING = Cingulata; DASY = Dasypodidae; DELP = Delphinidae; DERM = Dermoptera; Erob = <em>Eschrichtius robustus</em>; INIA = <em>Inia</em>; FOLI = Folivora; GALE = <em>Galeopterus</em>; LIPO = <em>Lipotes</em>; Lobl = <em>Lagenorhynchus obliquidens</em>; MANI = Manidae; MONO = Monodontidae; MYRM = Myrmecophagidae; MYST = Mysticeti; NPP = Not present in <em>Platanista</em> or Physeteroidea, but present in other Odontocetes; NPZ = Not present in Ziphiidae, but present in other Odontocetes; Oorc = <em>Orcinus orca</em>; PEUT = Tolypeutinae; PHOC = Phocoenidae; PHOL = Pholidota; PHOR = Chlamyphorinae; PILO = Pilosa; PHYS = Physeteroidea; PONT = <em>Pontoporia</em>; Schi = <em>Sousa chinensis</em>; SIRE = Sirenia; Tadu = <em>Tursiops aduncus</em>; TOLY = <em>Tolypeutes</em>; VERM = Vermilingua; XEN = Xenarthra. <br> <strong>- Supplementary_Table_S3.xlsx: </strong>Accession numbers and functionality of ASMT in species examined. See Table S2 caption for details. <strong>- Supplementary_Table_S4.xlsx: </strong>Accession numbers and functionality of MTNR1A in species examined. See Table S2 caption for details. <strong>- Supplementary_Table_S5.xlsx: </strong>Accession numbers and functionality of MTNR1B in species examined. See Table S2 caption for details. <strong>- Supplementary_Table_S6.xlsx: </strong>Codon frequency model selection. These are the results from one ratio dN/dS analyses using different codon frequency models. <strong>- Supplementary_Table_S7.xlsx: </strong>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 &lt; 0.05), model comparison bolded and given green background. For most models, w only shown for branch(es) of interest. <strong>- Supplementary_Table_S8.xlsx: </strong>Results of ASMT PAML dN/dS analyses. Refer to Table S7 caption for additional details. <strong>- Supplementary_Table_S9.xlsx: </strong>Results of MTNR1A PAML dN/dS analyses. Refer to Table S7 caption for additional details. <strong>- Supplementary_Table_S10.xlsx: </strong>Results of MTNR1B PAML dN/dS analyses. Refer to Table S7 caption for additional details. <strong>- Supplementary_Table_S11.xlsx: </strong>Results of BLASTing and mapping short reads from <em>Alligator mississippiensis</em> RNA sequencing experiments. <strong>- Supplementary_Dataset_S1_all_ali_fasta.txt: </strong>Genomic alignments in fasta format used to determine the pseudogene/functional status of the different genes in different taxonomic groups. <strong>- Supplementary_Dataset_S2_AANAT_RAxML_ali.phy: </strong>Alignment of AANAT in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. <strong>- Supplementary_Dataset_S3_ASMT_RAxML_ali.phy: </strong>Alignment of ASMT in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. <strong>- Supplementary_Dataset_S4_MTNR1A_MTNR1B_RAxML_ali.phy: </strong>Alignment of MTNR1A and MTNR1B in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. <strong>- Supplementary_Dataset_S5_AANAT_PAML_alig.fasta: </strong>Codon alignment of AANAT in fasta format used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S6_ASMT_PAML_ali.fasta: </strong>Codon alignment of ASMT in fasta format used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S7_MTNR1A_PAML_ali.fasta: </strong>Codon alignment of MTNR1A in fasta format used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S8_MTNR1B_PAML_ali.fasta: </strong>Codon alignment of MTNR1B in fasta format used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S9_PAML_topology.tre: </strong>Tree topology in newick format used in selection pressure analyses with PAML.<br>