Taxonomy based on limited genomic markers may underestimates species diversity of rockhopper penguins and threaten their conservation

Delimiting recently diverged species is challenging. During speciation,
genetic differentiation may be distributed unevenly across the genome, as
different genomic regions can be subject to different selective pressures
and evolutionary histories. Reliance on limited numbers of genetic markers
that may be underpowered can make species delimitation even more
challenging, potentially resulting in taxonomic inconsistencies.
Rockhopper penguins of the genus Eudyptes comprise three
broadly recognized taxa: northern (E. moseleyi), southern (E. chrysocome),
and eastern rockhopper (E. filholi). Their taxonomic status has been
controversial for decades, with researchers disagreeing about
whether E. chrysocome and E. filholiare
distinct species or conspecific. Our goal is to evaluate genome-wide
patterns of divergence to evaluate genetic differentiation and species
delimitation in rockhopper penguins, and to assess which
mechanisms may underlie previous discordance among nuclear versus
mitochondrial analyses. We generated reduced-representation
genomic libraries using Double Digest Restriction-site Associated DNA
(ddRAD) sequencing to evaluate genetic differentiation, contemporary
migration rates and admixture among colonies of rockhopper
penguins. The extent of genetic differentiation among the three
taxa was consistently higher than population-level genetic differentiation
found within these and other penguin species. There was no evidence of
admixture among the three taxa, suggesting the absence of ongoing gene
flow among them. Species delimitation analyses based on molecular data,
along with other lines of evidence, provide strong support for the
taxonomic distinction of three species of rockhopper
penguins. Our results provide strong support for the existence of
three distinct species of rockhopper penguins. The recognition of this
taxonomic diversity is crucial for the management and conservation of this
widely distributed species group. This study illustrates that widespread
dispersive seabird lineages lacking obvious morphological differences may
nevertheless have complex evolutionary histories and comprise cryptic
species diversity.