Abstract
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.
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Acknowledgements
Financial support for this study was provided by ANID Fondecyt postdoctorado 3240563, ANID Subvención a la Instalación en la Academia (SIA) 85250093, INACH RT_12-14, Fondecyt 1150517, PIA ACT172065 GAB, Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Millennium Institute Center of Genome Regulation (CRG), ANID - MILENIO ICN2021_002 and ICN2021_044, the CNPq (431463/2016-6) and the PROANTAR, IPEV programs 137 ANTAVIA and 354 ETHOTAAF and by the Spanish Research Agency (CGL2004-01348, CGL2007-60369, POL2006-06635 and CTM2015-64720-R). The Geryon cluster at the Centro de Astro-Ingeniería UC was extensively used for the calculations performed in this paper. The ANID BASAL project FB21000, BASAL CATA PFB-06, Anillo ACT-86, FONDEQUIP AIC-57, and QUIMAL 130008 provided funding for several improvements to the Geryon cluster. L.R.P. and M.G. were funded by the South African Department of Science and Innovation through the EU-Biodiversa ASICS project. The work conducted by HL was carried out in a nongovernmental capacity; the findings and conclusions in this article are those of the author(s) and do not necessarily represent the views of the U.S. Fish and Wildlife Service. We thank Sarah Crofts, Micky Reeves, and Jonathan Handley from Falklands Conservation for their contribution to the sampling. We thank Mark Adams (Natural History Museum, UK), Paul Sweet (American Museum of Natural History) and Judy Clarke (Tasmanian Museum and Art Gallery, Aust) for facilitating access to their gentoo penguin collections.
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Noll, D., Younger, J., Pertierra, L.R. et al. Integrative evidence reveals adaptive divergence and speciation in gentoo penguins. Commun Biol (2026). https://doi.org/10.1038/s42003-026-10081-7
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DOI: https://doi.org/10.1038/s42003-026-10081-7
