Let’s not hop to conclusions: Delineating species in the Rockhopper Penguin complex

There are three taxa in the Rockhopper Penguin complex. But are they all distinct species?

Just because you can differentiate between populations using genetic data doesn’t mean they should be considered separate species. The difficulty of delineating species was nicely discussed by Jeet Sukumaran and Lacey Knowles in a 2017 PNAS-paper. They showed that some methods for species delimitation – in their case the multispecies coalescent – mainly capture genetic population structure, but do not provide guidelines for drawing species boundaries. They concluded that “genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.”

I have expanded this conclusion in a book chapter, arguing that in order to delineate species, you need to understand the speciation process. This approach is nicely illustrated by a recent study in the Journal of Heredity that considers the taxonomy of Rockhopper Penguins (genus Eudyptes).


A Southern Rockhopper Penguin on Saunders Island, Falkland Islands © Ben Tubby | Flickr


Three Species?

The Rockhopper Penguin complex consists of two species: the Northern Rockhopper Penguin (E. moseleyi) and the Southern Rockhopper Penguin (E. chrysocome). The latter species contains two subspecies (chrysocome and filholi). However, some authors have suggested that these two subspecies should be elevated to species rank, because they can be separated based on several mitochondrial genes. But as I wrote in the beginning of this blog post: “Just because you can differentiate between populations using genetic data doesn’t mean they should be considered separate species.”

So, Herman Mays Jr. and his colleagues performed a phylogeographic study of the Rockhopper Penguins to gain more insights into their evolutionary history. This knowledge could then be used to better inform taxonomic decisions.


This haplotype network show that it is possible to discriminate between the three Rockhopper Pengiun taxa. But are they also different species? From: Mays et al. (2019) Journal of Heredity


Gene Flow

Analyses of the mitochondrial gene ND2 confirmed previous work: it is indeed possible to discriminate between the three taxa using mtDNA (see haplotype network above). But what about their evolutionary history? More detailed analyses indicated that Northern and Southern Rockhopper Penguins diverged about one million years ago and experienced a small (but significant) amount of gene flow. At around 0.5 million years ago, the two subspecies originated within the Southern Rockhopper Penguin. They showed high levels of gene flow.

These results can be interpreted in different ways. Currently, species concepts allow for some level of interspecific gene flow. But how much gene flow is too much? Perhaps some species delimitation software can help us out. A BPP (Bayesian Phylogenetics and Phylogeography) approach indicated that Northern and Southern Rockhopper Penguins should be considered separate species, while E. c. chrysocome and E. c. filholi do not qualify for an elevation to species rank.


Northern Rockhopper Penguin in Edinburgh Zoo, Scotland © Bardrock | Wikimedia Commons


Other Evidence

However, Jeet Sukumaran and Lacey Knowles already warned us not to take the results from species delimitation software at face value. What about other lines of evidence? The authors write the following:

We know of no evidence for separate species lineages in E. c. filholi and E. c. chrysocome outside of those suggested on the basis of mtDNA. There appear to be few if any fixed morphological, ecological, or behavioral differences between E. c. filholi and E. c. chrysocome outside of characters related to the coloration of the patch of skin at the base of the bill and any other phenotypic diversity that does exist among these taxa could likely be clinal.

More detailed studies are always welcome, but for now we can conclude that there are two species of Rockhopper Penguin.



Banks, J., Van Buren, A., Cherel, Y., & Whitfield, J. B. (2006). Genetic evidence for three species of rockhopper penguins, Eudyptes chrysocome. Polar Biology30(1), 61-67.

Mays Jr, H. L. et al. (2019). Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi). Journal of Heredity110(7), 801-817.

Ottenburghs, J. (2019). Avian species concepts in the light of genomics. In Avian Genomics in Ecology and Evolution (pp. 211-235). Springer, Cham.

Sukumaran, J., & Knowles, L. L. (2017). Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences114(7), 1607-1612.


This paper has been added to the Sphenisciformes page.

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