This repository provides the data, scripts, and figures for the analyses in "Genomic signatures of spatially divergent selection at clownfish range margins," which identifies the population structure and signatures of selection in populations of Amphiprion clarkii (the yellowtail clownfish) across the northern half of its range.

Citation: Clark RD, Aardema ML, Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes Jr. HR, Pinsky ML. (2021) Genomic signatures of spatially divergent selection at clownfish range margins. Proceedings of the Royal Society B: Biological Sciences. 288:20210407. (https://doi.org/10.1098/rspb.2021.0407)

This repository is organized into 3 folders:

1. /Data: Contains source data for R scripts, reference fasta, and metadata from sample collections.
2. /Scripts: Contains R scripts and code for analyses included in the manuscript.
3. /Plots: Contains pngs and tiffs of plots included in the manuscript, as well as additional plots for data exploration purposes.

Raw reads can be found in the GenBank short reads archive (BioProject PRJNA699463, SRA accession numbers SRR13627993–13628017).

Please contact René at rclark848[at]gmail.com with any questions.

Also available to download as a zip archive from DRYAD: https://doi.org/10.5061/dryad.5x69p8d30.

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Necessary Programs/Software for Bioinformatics

1. Bowtie (v.1.1.2)
2. BUSCO (v.5)
3. CD-HIT-EST (v.4.6.6)
4. GATK (v.3.8.1)
5. Picard Tools (v.1.119)
6. SAMtools (v.1.3.0)
7. Stampy (v.1.0.28)
8. Trinity (v.2.2.0)
9. VCFtools (v.1.16)

Necessary Programs/Software for Data Analysis

1. BAYPASS (v.2.1)
2. easySFS (v.1)
3. fastsimcoal2 (v.2.6)
4. PGDSpider (v.2.1.1.5)
5. plink (v.1.9)
6. R (v.3.4.4 or above)
7. RStudio (v.2022.12.0 or above)
8. SnpEff (v.4.5)
9. Stairway Plot (v.2)
10. STRUCTURE (v.2.3.4)
11. VCFtools (v.1.16)

Necessary R Packages

1. adegenet (v.2.1.10)
2. boot (v.1.3.28)
3. corrplot (v.0.92)
4. devtools (v.2.4.5)
5. ggpubr (v.0.6.0)
6. gridExtra (v.2.3)
7. gtable (v.0.3.1)
8. hierfstat (v.0.5.11)
9. mvtnorm (v.1.2.2)
10. pegas (v.1.2)
11. plotrix (v.3.8.2)
12. pophelper (v.2.3.1)
13. purrr (v.1.0.1)
14. readr (v.2.1.4)
15. related (v.0.7)
16. robust (v.0.7.1)
17. tidyverse (v.2.0.0)
18. vcfR (v.1.14.0)
19. vegan (v.2.6.4)