Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories

<p>The following files are contained in this repository:</p> <p><br> README.Hume_et_al_2022.zenodov4.txt - This document.</p> <p>scripts.Hume_et_al_2022.zenodov4.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript.</p> <p>acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study.</p> <p>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.</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as &#39;raw&#39; in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as &#39;linked&#39; in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as &#39;unlinked&#39; in the Methods of the associated manuscript.</p> <p>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.</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as &#39;raw&#39; in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as &#39;linked&#39; in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as &#39;unlinked&#39; in the Methods of the associated manuscript.</p> <p>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.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as &#39;raw&#39; in the Methods of the associated manuscript.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs.</p> <p>Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as &#39;target genes&#39; in the Methods of the associated manuscript.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome.</p> <p>&nbsp;</p> <p>mtORF Phylogeny</p> <p>TP-Johnston_mtORF-Pocillo.fa = all sequences</p> <p>TP-Johnston_mtORF-Pocillo.mafft.fa = mafft alignment</p> <p>TP-Johnston_mtORF-Pocillo.mafft.ML.nwk = ML tree newick</p> <p>&nbsp;</p> <p>Hellberg genotype network Porites</p> <p>TP-Hellberg_MM32-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_MM100-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_ATPaseB.nex = all aligned sequences for this locus with indels encoded,</p> <p>TP-Hellberg_POFAD.nex = POFAD multilocus genotypic distance,</p> <p>TP-Hellberg_Splitstree.nex= Multilocus genotype network in nexus format</p> <p><br> Gradient Forest Analysis</p> <p>Poc_abund.csv - Pocillopora SSH Occurrences per Site er Island</p> <p>Por_abund.csv - Porites SSH Occurrences per Site er Island</p> <p>mean_depth_por.csv - per site per island mean depth among Porites colonies</p> <p>mean_depth_poc.csv - per site per island mean depth among Pocillopora colonies</p>