Integrative evidence reveals adaptive divergence and speciation in gentoo penguins.

Understanding lineage divergence is crucial for uncovering cryptic biodiversity. Adaptive divergence, geographic isolation and life-history traits drive speciation in heterogeneous environments. The gentoo penguin complex (Pygoscelis spp.), historically treated as a single species, provides an ideal system to examine divergence across its full distribution. Here, we show the existence of four divergent evolutionary lineages (northern, southern, southeastern, and eastern), supported by phylogenomic and lineage-specific selective pressures, despite ancestral gene flow. South Georgia and Macquarie individuals whose status has been debated, were included. Genomic scans reveal lineage-specific signals of positive selection in genes related to thermoregulation, oxygen transport, metabolism, and skeletal development, consistent with ecological and morphological differentiation across the Antarctic Polar Front. Future niche projections indicate severe habitat losses for three lineages, whereas the southern gentoo may expand its range. We propose a taxonomic revision recognizing four distinct gentoo penguin species, including Pygoscelis kerguelensis sp. nov., with important conservation implications.