Genomics Reveals Extensive Population Structure and Undescribed Phylogenetic Relationships in the Cascade Torrent Salamander ( <i>Rhyacotriton cascadae</i> )

ABSTRACT Aim Aims of the study are to examine patterns of range‐wide genetic differentiation and population structure in a headwater obligate salamander living in a geologically rich region, to identify genetically distinct populations and areas of gene flow between them. Location Oregon and Washington in the Pacific Northwest, United States of America. Time Period Tissue samples were collected in 2022 and 2023. Major Taxa Studied The Cascade torrent salamander Rhyacotriton cascadae . Methods Utilisation of a genome‐wide single nucleotide polymorphism (SNP) dataset from across the species range to conduct a principal components analysis (PCA), Bayesian model of population structure, co‐ancestry matrix, phylogenetic tree and estimate genetic diversity. Results There are extensive levels of population structure within R. cascadae , including a previously unknown and highly differentiated clade. Structure is characterised by an island‐like pattern wherein the species is comprised of six populations that function as independent demographic units, with gene flow largely constrained within populations. Main Conclusions Our findings reveal cryptic population structure within R. cascadae , identifying six distinct populations across the range. The northernmost population in the northwest of the species range in Washington is surprisingly highly divergent from the other five populations, and the divergence was not previously known to science. While major rivers act as phylogeographic boundaries between some populations, these boundaries appear to not always be complete.