Data and scripts: Genetic recapture of Holothuria whitmaei on Lizard island
Updated: 2026-08-31
Genetic data and ecological data and R scripts for publication: "Uthicke, S, Gomez Cabrera, M, Byrne, M, Purcell, S. 2026. Extreme longevity revealed by 24-year genetic mark–recapture challenges conservation of endangered sea cucumbers. iScience" 2 data sets and 6 R scripts. Data: 1) vcf file produced by AGRF bioinformaticists, based on sequencing data deposited at: Sequencing was performed on 10B 300 cycle lanes on the Illumina NovaSeq X platform, yielding 150 bp paired end reads. Initial bioinformatics was conducted at AGRF using the DeNovoGBS function from NGSEP Version 4.2.0 (07/01/2022) 56 resulting in a vcf file with 224,347 SNPs. Raw sequence data are available at NCBI National Library of Medicine (Biosample accession numbers SAMN60877514- SAMN60877674) 2) size of weight measurements of holothrurians at three points in time
Data
- R-script Size comparison and t-test
- R-script Survival Mortality and bootstrap calculations
- genotype file supplied by AGRF [vcf file size: 1.38 GB]
- R-script - Filters data, produces input for second genetic script
- R-script - Produces supplementary Figure
- R Script: Produces Fig. 3 in manuscript
- R-script - Produces Fig. 1 and Fig. 2
- Size data - Input file for script
- Full metadata link
- http://i.creativecommons.org/l/by-nc/3.0/au/88x31.png
- http://creativecommons.org/licenses/by-nc/3.0/au/
