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> 1:75. doi:10.12688/openreseurope.13795.1. <strong>Supplementary File Legends:</strong> <strong>- Supplementary_Figure_S1.pdf:</strong> <em>AANAT</em> PAML ‘master model’ showing branch categories, corresponding to “Model 1: 24 ratio” in Supplementary Table S7. <strong>- Supplementary_Figure_S2.pdf:</strong> <em>ASMT</em> PAML ‘master model’ showing branch categories, corresponding to “Model 2: 24 ratio” in Supplementary Table S8. <strong>- Supplementary_Figure_S3.pdf:</strong> <em>MTNR1A</em> PAML ‘master model’ showing branch categories, corresponding to “Model 1: 27 ratio” in Supplementary Table S9. <strong>- Supplementary_Figure_S4.pdf:</strong> <em>MTNR1B</em> PAML ‘master model’ showing branch categories, corresponding to “Model 1: 46 ratio” in Supplementary Table S10. <strong>- Supplementary_Figure_S5.pdf:</strong> RAxML <em>AANAT</em> gene tree. Numbers at nodes correspond to bootstrap support values. <strong>- Supplementary_Figure_S6.pdf: </strong>RAxML <em>ASMT</em> gene tree. Numbers at nodes correspond to bootstrap support values. <strong>- Supplementary_Figure_S7.pdf: </strong>RAxML <em>MTNR1A</em>+<em>MTNR1B</em> tree. Numbers at nodes correspond to bootstrap support values. <strong>- Supplementary_Figure_S8.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> exon 2 in cetaceans. Read Supplementary Table S13 for further details. <strong>- Supplementary_Figure_S9.pdf: </strong>Supporting data showing the inactivation of <em>ASMT</em> in spalacids and <em>Fukomys damarensis</em>. Read Supplementary Table S13 for further details. <strong>- Supplementary_Figure_S10.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in hyracoids and <em>Cyclopes didactylus</em>. Read Supplementary Table S13 for further details. <strong>- Supplementary_Figure_S11.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in sirenians. Read Supplementary Table S13 for further details. <strong>- Supplementary_Figure_S12.pdf: </strong>Supporting data showing the inactivation of <em>AANAT</em> in sirenians and a polymorphic premature stop codon in exon 5 of <em>ASMT</em> in <em>Trichechus manatus</em>. Read Supplementary Table S13 for further details. <strong>- Supplementary_Figure_S13.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in <em>Condylura cristata</em>. Read Supplementary Table S13 for further details. <strong>- Supplementary_Figure_S14.pdf: </strong>Supporting data showing the inactivation of <em>MTNR1A</em> in <em>Phataginus tricuspis</em>. Read Supplementary Table S14 for further details. <strong>- Supplementary_Figure_S15.pdf: </strong>PAML <em>AANAT</em> results, Model 1: 24 ratio (see Supplementary Table S7). <strong>- Supplementary_Figure_S16.pdf: </strong>PAML <em>ASMT</em> results, Model 2: 24 ratio (see Supplementary Table S8). <strong>- Supplementary_Figure_S17.pdf: </strong>PAML <em>MTNR1A</em> results, Model 1: 27 ratio (see Supplementary Table S9). <strong>- Supplementary_Figure_S18.pdf: </strong>PAML <em>MTNR1B</em> results, Model 1: 46 ratio (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, with accession prefix provided; Whole Genome Sequencing of Short Reads: whole genomes were sequenced using short-read technologies. The methodologies varied for the species, and will be or have been published with other projects, so please contact the author(s) for information on the specific methodology and samples used (Xenarthrans, <em>Proteles cristatus</em>, <em>Otocyon megalotis</em>: Frédéric Delsuc, e-mail: [e-mail]; Crocodylians: John Gatesy, e-mail: [e-mail]; <em>Dugong dugon</em>: Mark Springer, e-mail: [e-mail]; 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/). Coverage: indicates coverage of the whole genome (reported in NCBI or other source) or individual genes (derived from short read mapping). Scaffold and contig N50: reported in NCBI or other source. <strong>- Supplementary_Table_S2.xlsx: </strong>Accession numbers and functionality of <em>AANAT</em> in species examined. If Accession # indicated as “New”, sequence generated for this study and can be found in Supplementary Dataset S1. Parentheses after accession number indicates coordinates for sequence on the contig / scaffold. Exon colors code for the following: green = putatively functional; yellow = missing (e.g., negative BLAST results, negative mapping results); 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 <em>ASMT</em> in species examined. See Table S2 caption for details. <strong>- Supplementary_Table_S4.xlsx: </strong>Accession numbers and functionality of <em>MTNR1A</em> in species examined. See Table S2 caption for details. <strong>- Supplementary_Table_S5.xlsx: </strong>Accession numbers and functionality of <em>MTNR1B</em> 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. AIC = Akaike Information Criterion. <strong>- Supplementary_Table_S7.xlsx: </strong>Results of <em>AANAT</em> PAML dN/dS analyses for mammals. Model: BG = branch(es) grouped with background; fixed 1 = branch(es) fixed at 1. p’-value: p-value after Holm-Bonferroni correction for multiple testing. Model Comparison: if model comparison yields statistically significant differences (p &lt; 0.05), model comparison bolded and given green background; if model comparison is still significant after Holm-Bonferroni correction, asterisk (*) added. For most models, w only shown for branch(es) of interest. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S1. <strong>- Supplementary_Table_S8.xlsx: </strong>Results of <em>ASMT</em> PAML dN/dS analyses for mammals. Refer to Table S7 caption for additional details. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S2. <strong>- Supplementary_Table_S9.xlsx: </strong>Results of <em>MTNR1A</em> PAML dN/dS analyses for mammals. Refer to Table S7 caption for additional details. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S3. <strong>- Supplementary_Table_S10.xlsx: </strong>Results of <em>MTNR1B</em> PAML dN/dS analyses for mammals. Refer to Table S7 caption for additional details. Numbers in front of taxonomic names in first row correspond to numbers in the master model shown in Supplementary Figure S4. <strong>- Supplementary_Table_S11.xlsx: </strong>Results of PAML analyses for sauropsids. <strong>- Supplementary_Table_S12.xlsx: </strong>Results of BLASTing and mapping short reads from <em>Alligator mississippiensis</em> RNA sequencing experiments. <strong>- Supplementary_Table_S13.xlsx: </strong>Supporting data for validating putative inactivating mutations. Validating data came from four general sources of information: mutations shared by more than one species within a clade, mutations shared by two sources of sequencing data for the same species, mutations validated by coverage of mapped short reads and statistically elevated dN/dS ratio estimates. For additional details, see Supplementary Tables S2–S5 and S7–S10, as well as Figure 2 and Supplementary Figures S8–S18. <strong>- Supplementary_Dataset_S1.txt:</strong><strong> </strong>Genomic alignments in fasta format used to determine the pseudogene/functional status of all four melatonin genes in different taxonomic groups. <strong>- Supplementary_Dataset_S2.txt:</strong><strong> </strong>Alignment of <em>AANAT</em> in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. <strong>- Supplementary_Dataset_S3.txt: </strong>Alignment of <em>ASMT</em> in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. <strong>- Supplementary_Dataset_S4.txt: </strong>Alignment of <em>MTNR1A</em> and <em>MTNR1B</em> in phylip format used in maximum likelihood phylogenetic reconstruction with RAxML. <strong>- Supplementary_Dataset_S5.txt:</strong><strong> </strong>Codon alignments of <em>AANAT</em> used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S6.txt: </strong>Codon alignments of <em>ASMT</em> used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S7.txt:</strong><strong> </strong>Codon alignments of <em>MTNR1A</em> used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S8.txt: </strong>Codon alignments of <em>MTNR1B</em> used in selection pressure analyses with PAML. <strong>- Supplementary_Dataset_S9.txt: </strong>Tree topologies in newick format used in selection pressure analyses with PAML.