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:...
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ftzenodo:oai:zenodo.org:4894212 2024-09-15T18:00:16+00:00 Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals Emerling, Christopher A. Springer, Mark S. Gatesy, John Jones, Zachary Hamilton, Deana Xia-Zhu, David Collin, Matthew A. Delsuc, Frédéric 2021-06-03 https://doi.org/10.5281/zenodo.4894212 eng eng Zenodo https://doi.org/10.5281/zenodo.4894211 https://doi.org/10.5281/zenodo.4894212 oai:zenodo.org:4894212 info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode Open Research Europe, (2021-06-03) Mammals Melatonin pathway Molecular evolution Pseudogenes Convergence Pineal gland Crocodilians info:eu-repo/semantics/other 2021 ftzenodo https://doi.org/10.5281/zenodo.489421210.5281/zenodo.4894211 2024-07-26T14:19:21Z 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+MTNR1Btree. - 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 ... Other/Unknown Material bowhead whale Zenodo |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
English |
topic |
Mammals Melatonin pathway Molecular evolution Pseudogenes Convergence Pineal gland Crocodilians |
spellingShingle |
Mammals Melatonin pathway Molecular evolution Pseudogenes Convergence Pineal gland Crocodilians Emerling, Christopher A. Springer, Mark S. Gatesy, John Jones, Zachary Hamilton, Deana Xia-Zhu, David Collin, Matthew A. Delsuc, Frédéric Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals |
topic_facet |
Mammals Melatonin pathway Molecular evolution Pseudogenes Convergence Pineal gland Crocodilians |
description |
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+MTNR1Btree. - 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 ... |
format |
Other/Unknown Material |
author |
Emerling, Christopher A. Springer, Mark S. Gatesy, John Jones, Zachary Hamilton, Deana Xia-Zhu, David Collin, Matthew A. Delsuc, Frédéric |
author_facet |
Emerling, Christopher A. Springer, Mark S. Gatesy, John Jones, Zachary Hamilton, Deana Xia-Zhu, David Collin, Matthew A. Delsuc, Frédéric |
author_sort |
Emerling, Christopher A. |
title |
Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals |
title_short |
Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals |
title_full |
Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals |
title_fullStr |
Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals |
title_full_unstemmed |
Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals |
title_sort |
genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals |
publisher |
Zenodo |
publishDate |
2021 |
url |
https://doi.org/10.5281/zenodo.4894212 |
genre |
bowhead whale |
genre_facet |
bowhead whale |
op_source |
Open Research Europe, (2021-06-03) |
op_relation |
https://doi.org/10.5281/zenodo.4894211 https://doi.org/10.5281/zenodo.4894212 oai:zenodo.org:4894212 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.5281/zenodo.489421210.5281/zenodo.4894211 |
_version_ |
1810437428577566720 |