Genomic differentiation of endangered polyploid Braya (Brassicaceae) populations in the limestone barrens ecosystem at risk support separate management units
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Endangered species recovery benefits from robust genetic insights. Braya longii and B. fernaldii are morphologically distinct but closely related octoploid self-fertilizing species, restricted to the island of Newfoundland’s globally rare limestone barrens. Despite distinct morphology, they are currently managed under a unified recovery plan due to ecological similarity. We assessed genetic diversity, inbreeding, population structure, management units (MUs), evolutionary significant units (ESUs), and demographic history to inform long-term conservation. Using genotyping-by-sequencing, we obtained 92,671 SNPs from 85 individuals across eight populations. Results revealed variable genetic diversity, low to moderate population differentiation within and between species, and support that B. longii is distinct and evolved from B. fernaldii . Phylogenetic and structure analyses showed strong population structuring and relationship patterns that do not conform with geographic distance. Despite bioinformatic filtering of homologous variants with GBS-SNP-CROP, parameter estimation in polyploids remained uncertain, with elevated heterozygosity and biased effective population sizes, highlighting the need for improved analytical tools for polyploid genomics. Our analyses support one ESU encompassing both species and seven MUs, critical for guiding augmentation, reintroduction, and translocation strategies. This study demonstrates that narrow endemic polyploids can show complex genetic patterns shaped by demographic history and anthropogenic disturbance. These results provide essential genomic guidance for the recovery of Braya species and restoration of the limestone barrens ecosystem.