Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within <i>Eucalyptus salubris</i>

Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, often criticized because they typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we Eucalyptus salubris unexpectedly two divergent lineages but was sampled sufficiently make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) investigate whether purported remain discrete genetic entities if intergrade throughout species’ range. also assessed morphological ecological traits, sequenced chloroplast DNA. SNP results showed strong genome-wide divergence (FST = 0.252) between lineages: one dominated north southern regions Within lineages, gene flow high, with low differentiation (mean FST 0.056) spanning hundreds kilometers. In central region, were interspersed maintained distinctiveness: indirect demonstration reproductive isolation. Populations lineage exhibited significantly lower specific leaf area occurred on soils phosphorus relative northern lineage. Finally, major haplotypes associated each shared in distribution. Together, these suggest have non-contemporary origins ecotypic adaptive processes strengthened more recently. conclude warrant taxonomic recognition as separate species provide fascinating insight into eucalypt speciation.