DOI: 10.5281/zenodo.7665832
title: Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories

description: The following files are contained in this repository: README.Hume_et_al_2022.zenodov2.txt - This document. Voolstra_etal_23.zenodov2.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript. acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study. TaraPacific_SST_timeseries_mean_productsV2mai2021.Hume_et_al_2022.zenodov1.csv - The historical temperature data set used for the RDA, Mantel tests and gradient Forest analysis. Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html). Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs. Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript. Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs. Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript. Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs. Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html). Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs. Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript. Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs. Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript. Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs. PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as 'raw' in the Methods of the associated manuscript. PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs. Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as 'target genes' in the Methods of the associated manuscript. Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome. Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome. mtORF Phylogeny TP-Johnston_mtORF-Pocillo.fa = all sequences TP-Johnston_mtORF-Pocillo.mafft.fa = mafft alignment TP-Johnston_mtORF-Pocillo.mafft.ML.nwk = ML tree newick Gradient Forest Analysis Poc_abund.csv - Pocillopora SSH Occurrences per Site er Island Por_abund.csv - Porites SSH Occurrences per Site er Island mean_depth_por.csv - per site per island mean depth among Porites colonies mean_depth_poc.csv - per site per island mean depth among Pocillopora colonies REFERENCES<br> Lan, D., et al. (2022) Genozip 14 - advances in compression of BAM and CRAM files (preprint) bioRxiv, doi:10.1101/2022.09.12.507582 Lan, D., et al. (2022) Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations (preprint) bioRxiv 10.1101/2022.07.17.500374 Lan, D (2021) The Variant Call Format - Dual Coordinates Extension (DVCF) Specification (preprint) doi:10.6084/m9.figshare.14685816 Lan, D., et al. (2021) Genozip: a universal extensible genomic data compressor Bioinformatics, 37, 2225–2230 Lan, D., et al. (2020) genozip: a fast and efficient compression tool for VCF files Bioinformatics, 36, 4091–4092
description: Special thanks to the Tara Ocean Foundation, the R/V Tara crew and the Tara Pacific Expedition Participants (https://doi.org/10.5281/zenodo.3777760). We are keen to thank the commitment of the following institutions for their financial and scientific support that made this unique Tara Pacific Expedition possible: CNRS, PSL, CSM, EPHE, Genoscope, CEA, Inserm, Université Côte d'Azur, ANR, agnès b., UNESCO-IOC, the Veolia Foundation, the Prince Albert II de Monaco Foundation, Région Bretagne, Billerudkorsnas, AmerisourceBergen Company, Lorient Agglomération, Oceans by Disney, L'Oréal, Biotherm, France Collectivités, Fonds Français pour l'Environnement Mondial (FFEM), Etienne Bourgois, and the Tara Ocean Foundation teams. Tara Pacific would not exist without the continuous support of the participating institutes. The authors also particularly thank Serge Planes, Denis Allemand, and the Tara Pacific consortium.
description: {"references": ["Lan, D., et al. (2022) Genozip 14 - advances in compression of BAM and CRAM files (preprint) bioRxiv, doi:10.1101/2022.09.12.507582", "Planes, et al., (2019) The Tara Pacific expedition\u2014A pan-ecosystemic approach of the \"-omics\" complexity of coral reef holobionts across the Pacific Ocean, PLOS Biology, doi:https://doi.org/10.1371/journal.pbio.3000483"]}