Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Version 1.1
Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Louis, Marie; Korlević, Petra; Nykänen, Milaja; Archer, Frederick; Berrow, Simon; Brownlow, Andrew; Lorenzen, Eline; O'brien, Joanne; Post, Klaas; Racimo, Fernando; Rogan, Emer; Rosel, Patricia; Sinding, Mikkel; Van Der Es, Henry; Wales, Nathan; Fontaine, Michael C.; Gaggiotti, Oscar; Foote, Andrew, 2023, "Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters", https://doi.org/10.23708/DABAWD, DataSuds, V1
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Description

This dataset includes the data and scripts supporting the replicability of the paper: Louis M.*, Korlević P.*, Nykänen M.*, Archer F., Berrow S., Brownload A., Lorenzen E. D., O’Brien J., Post K., Racimo F., Rogan E., Rosel P. E., Sinding M.-H. S., van der Es H., Wales N., Fontaine M. C.**, Gaggiotti O. E.**, Foote A. D.** Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nature Communications, in press. (*joint first author ; **joint senior author)

Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenomics to understand the tempo and independence of parallel coastal ecotype adaptation in common bottlenose dolphins (Tursiops truncatus). For this, we generated whole genome re-sequencing data from subfossil dolphins (8,610-5,626 years BP) originating from around the formation time of new coastal habitat and compared them with data from contemporary populations.

(2023-06-05)
Subject Earth and Environmental Sciences; Medicine, Health and Life Sciences
Keyword dolphin, paleogenomics, adaptation, evolution, environment, coastal habitat
Related Publication Louis M., Korlević P., Nykänen M., Archer F., Berrow S., Brownload A., Lorenzen E. D., O’Brien J., Post K., Racimo F., Rogan E., Rosel P. E., Sinding M.-H. S., van der Es H., Wales N., Fontaine M. C., Gaggiotti O. E., Foote A. D. (2023) Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nature Communications 14, 4020. doi: 10.1038/s41467-023-39532-z
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Louis_et_al2023_3.1.1.smartpca_fromvcf.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 41.6 MB
Published Jun 9, 2023
19 Downloads
MD5: edeb5067263a9c6545e0ebbf479817d1
Input file and scripts to format a vcf file and run smartpca (Figure S4). To uncompress, type "tar xzvf 3.1.1.smartpca_fromvcf.tar.gz"
CodeData
Louis_et_al2023_3.1.2.smartpca_fromhaplo.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 29.7 MB
Published Jun 9, 2023
20 Downloads
MD5: 7f3a8762ab2f1393f629b9061ed84167
Scripts and input files to format an haplo file and run smartpca both for the data mapped to the killer whale reference genome and bottlenose dolphin reference genome (see subfolder mapped_Ttruncatus) (Figures 1c, S5 and S6). To uncompress, type "tar xzvf 3.1.2.smartpca_fromhaplo.tar.gz"
CodeData
Louis_et_al2023_3.2.single_read_PCA.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 16.2 KB
Published Jun 9, 2023
22 Downloads
MD5: 38529e12e86c2043ba0147206cb23475
Scripts and input files to run and plot a single-read PCA (Figure S8). To uncompress, type "tar xzvf 3.2.single_read_PCA.tar.gz"
CodeData
Louis_et_al2023_3.3.tfa.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 1.1 MB
Published Jun 9, 2023
20 Downloads
MD5: 1d4689415c6c66efd15ac30ad8866e16
Scripts and input file to run and plot the tfa - factor analysis (Figures 1d and S7). To uncompress, type "tar xzvf 3.3.tfa.tar.gz"
CodeData
Louis_et_al2023_3.4.PCA_downsampling_modern.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 13.1 MB
Published Jun 9, 2023
18 Downloads
MD5: 39d6bc3f6db277efe72dc0fb0dd72e8d
Scripts and input files to run smartpca (subfolder 3.4.1.smartpca) and the single read PCA (subfolder 3.4.2.single_read) on the modern data including one individual downsampled to 0.03x (Figure S3). To uncompress, type "tar xzvf 3.4.PCA_downsampling_modern.tar.gz"
CodeData
Louis_et_al2023_4.1.D_statistics.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 12.8 KB
Published Jun 9, 2023
21 Downloads
MD5: 068eb49f9c9aaeb60632c4cde49783ca
Scripts and input files to run D-statistics (Figures S9 and S10). To uncompress, type "tar xzvf 4.1.D_statistics.tar.gz"
CodeData
Louis_et_al2023_4.2.qpbrute.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 21.9 MB
Published Jun 9, 2023
22 Downloads
MD5: 823c1555aa862779e58967acee925a6c
Scripts and input file to format the files and run qprbute from an haplo file (subfolder 4.2.1.pseudohaploid_withSP1060) or a vcf file (subfolder 4.2.2.genotypes_modern) (Figure 2 and S11). To uncompress, type "tar xzvf 4.2.qpbrute.tar.gz"
CodeData
Louis_et_al2023_5.selection.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 7.8 MB
Published Jun 9, 2023
18 Downloads
MD5: 19899db3c096b4cc9e222b9477f727ea
Scripts and input files to run and plot heterozygosity (subfolder 5.1.heterozygosity), and genotype plots, NJ tree (including bootstrapping) and PCA (subfolder P5.2.CA_NJtree_genotype_plot) for the SNPs under parallel linked selection. There is aslo a subfolder within 5.2. to generate a NJ tree for the same number of randomly sampled neutral SNPs. This produces Figures 3, S12, S13 and S14. To uncompress, type "tar xzvf 5.selection.tar.gz"
CodeData
Louis_et_al2023_6.mitogenomes.tar.gz
Louis_et_al2023_Ancient_dolphin_genomes/Gzip Archive - 299.5 KB
Published Jun 9, 2023
20 Downloads
MD5: a870965b07accdc346cfbb09c65b1a7d
Scripts and input files to generate the mitogenone analyses (Figure S1). R script and files to plot the samples (Figure 1a). To uncompress, type "tar xzvf 6.mitogenomes.tar.gz"
CodeData
Louis_et_al2023_code_data_analyses.txt
Louis_et_al2023_Ancient_dolphin_genomes/Plain Text - 45.4 KB
Published Jun 9, 2023
35 Downloads
MD5: 7bb222a264abcc01418451e30dfaf646
Scripts, tools, and data to reproduce all the analyses in the manuscript
CodeDocumentation
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