The provenance assignment success of the DArTcap markers was tested with asssignPOP v. 1.2.2 (Chen, Marschall, et al., 2018 (link)) and rubias v.0.3.2 (Anderson et al., 2008 (link); Moran & Anderson, 2019 (link)). Assignment accuracy was tested with assignPOP, using both the Monte‐Carlo and K‐fold cross‐validation procedures to test the assignment of a hold‐out data set with 1000 iterations. We tested power of the markers by selecting a subset of loci with the highest FST values (5%, 10%, 50%, and 100% of all loci) to train the assignment model. Similarly, the assignment accuracy of simulated mixed groups, based on a reference leave‐one‐out dataset, was evaluated with rubias (Anderson et al., 2008 (link)). Known simulated proportions for each reporting unit were compared with the numbers estimated by rubias. Populations with a sample size of one (i.e., Sierra Leone, eastern Atlantic) were excluded from these analyses. We also examined the minimum number of informative markers needed to assign provenance by subsampling 5–500 markers based on loading contributions of each principal component from the DAPC analysis and testing the assignment accuracy with rubias.
Devloo‐Delva F., Burridge C.P., Kyne P.M., Brunnschweiler J.M., Chapman D.D., Charvet P., Chen X., Cliff G., Daly R., Drymon J.M., Espinoza M., Fernando D., Barcia L.G., Glaus K., González‐Garza B.I., Grant M.I., Gunasekera R.M., Hernandez S., Hyodo S., Jabado R.W., Jaquemet S., Johnson G., Ketchum J.T., Magalon H., Marthick J.R., Mollen F.H., Mona S., Naylor G.J., Nevill J.E., Phillips N.M., Pillans R.D., Postaire B.D., Smoothey A.F., Tachihara K., Tillet B.J., Valerio‐Vargas J.A, & Feutry P. (2023). From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator. Ecology and Evolution, 13(2), e9837.
Publication 2023
Dapc Rubias
Corresponding Organization : CSIRO Oceans and Atmosphere
Other organizations :
Charles Darwin University, Institute for Independent Studies Zürich, Florida International University, Universidade Federal do Ceará, South China Agricultural University, University of KwaZulu-Natal, South African Institute for Aquatic Biodiversity, South African Association for Marine Biological Research, Mississippi State University, Universidad de Costa Rica, Blue Resources Trust, University of the South Pacific, James Cook University, Universidad Veritas, Universidad Católica del Norte, The University of Tokyo, Elasmo Project, Ifremer, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Écologie Marine Tropicale des Océans Pacifique et Indien, Sorbonne Université, Université Paris Sciences et Lettres, École Pratique des Hautes Études, Institut de Systématique, Évolution, Biodiversité, University of Florida, Florida Museum of Natural History, University of Seychelles, University of Southern Mississippi, Sydney Institute of Marine Science, University of the Ryukyus, Translational Research Institute, University of Queensland
Proportion of loci with the highest F_ST values (5%, 10%, 50%, and 100% of all loci)
dependent variables
Assignment accuracy of the DArTcap markers
Assignment accuracy of simulated mixed groups
control variables
Monte-Carlo and K-fold cross-validation procedures to test the assignment of a hold-out data set
Reference leave-one-out dataset for simulated mixed groups
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