Abstract
AbstractAimDelimiting 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 genusEudyptescomprise 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 whetherE. chrysocomeandE. 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.LocationSub‐Antarctic and temperate coastal regions of the Southern Hemisphere.MethodsWe 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.ResultsThe 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.Main conclusionsOur 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.
Highlights
Accurate delimitation of species is essential for the management and conservation of biodiversity (Agapow et al, 2004; Frankham et al, 2012)
In addition to evaluating genetic differentiation and species delimitation of E. moseleyi, E. filholi and E. chrysocome, we evaluate contemporary migration rates and search for evidence of admixture based on prior suggestions about ongoing gene flow among rockhopper penguins (Mays et al, 2019)
We further explored the genetic relatedness of these outliers to all other sampled individuals via an identity-by-state analysis using SNPRELATE V. 1.20.1 (Zheng et al, 2012)
Summary
Accurate delimitation of species is essential for the management and conservation of biodiversity (Agapow et al, 2004; Frankham et al, 2012). Conflicting with the above, Mays et al (2019) suggested that E. filholi and E. chrysocome should be considered conspecific, in agreement with the two-species hypothesis, as their species delimitation analyses did not find sufficient differences to discriminate among the taxa, and analyses of migration rates between colonies suggested ongoing gene flow Such conclusions were based on the analysis of only six nuclear introns, and their species delimitation analysis could not discriminate the even more divergent and widely accepted split (around 5 Mya) between macaroni (E. chrysolophus) and rockhopper penguins; only one out of their four Genealogical Diversity Index (GDI) scenarios exceeded the 0.2 GDI threshold for recognizing potential species, but it did not reach the 0.7 GDI threshold for a strongly divergent species lineage. The conservation actions proposed by the IUCN include the determination of the taxonomic status of E. filholi and E. chrysocome, representing a key data source for the development of conservation plans for these charismatic birds
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