Where did all these penguins come from?

Genomic analyses unravel the evolutionary history of these flightless diving birds.

The evolution of penguins (order Sphenisciformes) remains a mystery. Different genetic studies disagree about the evolutionary relationships between particular species, the timing of speciation events and the original distribution of these iconic seabirds. The divergence time of the crown group (all living representatives of the penguins) ranges from 9.9 million years ago (during the Miocene) to 47.6 million years ago (during the Eocene). And the exact area of origin is also a matter of debate: some ornithologists suggest Antarctica with a subsequent expansion into warmer waters, while others point to Australia or New Zealand followed by colonization of the colder Antarctica. One way to settle these debates is to bring out the big guns: genomic data. A recent study in the journal PNAS applied this strategy and analyzed 22 genomes, representing 18 penguin species. Time to find out what they discovered about the evolution of penguins – a word that Benedict Cumberbatch has some difficulty pronouncing (see video below).

From Australia to Antarctica?

Let’s start with the most likely area of origin for penguins. The authors reconstructed the ancestral distributions of the sampled species and identified the coastlines of Australia, New Zealand, and nearby islands as the original range of the ancestor of extant penguins. From there, these birds colonized Antarctica and South America where they diversified into several species. The genomic analyses provide estimates for the timing of these events.

The first branching event led to the establishment of the genus Aptenodytes in the Antarctic, and reconstructions of the ancestral Pygoscelis species indicate that they colonized the Antarctic Peninsula soon after Aptenodytes, pointing to a long history of Antarctic occupation. In the mid-Miocene, the lineage leading to the Spheniscus/Eudyptula ancestor colonized the South American coast, with members of the genera Eudyptes, Eudyptula, Megadyptes, and Spheniscus progressively diversifying and colonizing warmer at-sea environments.

During the cooling event at the transition of the Pliocene and Pleistocene (about 2.5 million years ago), ice shelves expanded across the Southern Ocean, probably reducing connectivity between several penguin populations. This culminated in more speciation events within the genera Pygoscelis, Spheniscus, Eudyptes and Aptenodytes. The figure below provides a nice overview of all these events.

The evolutionary history of penguins based on genomic data. Reconstruction of ancestral distributions (the colored letters on the nodes in the tree) suggest that the ancestor of modern penguins lived in Australia and New Zealand. From: Vianna et al. (2020) PNAS.

Genes Going with the Flow

The phylogenetic tree from the genomic analyses largely agreed with another recent study based on complete mitochondrial genomes (which I also covered on this blog). A few differences between these studies can be explained by hybridization between several penguin species. The researchers write that “some of the main episodes of genomic introgression were detected among erect-crested and the ancestral rockhopper penguin species (17 to 23%), erect-crested and macaroni/royal penguins (25%), and the Gal√°pagos/Humboldt ancestor and Magellanic penguins (11%).” Interestingly, the direction of introgression in some of these species followed the clockwise flow of the Antarctic Circumpolar Current, the ocean current that circles around Antarctica. Individual penguins might have drifted off during foraging trips and were transported to nearby populations where they interbred with another resident species. Quite literally, gene flow.

This study nicely illustrates the power of genomic analyses. There is an enormous treasure of information hidden in the seemingly meaningless strings of A, T, G and C. With clever methods and careful analyses we are now able to find meaning in these DNA sequences and reconstruct the wonderful evolutionary history of life on our planet.

Patterns of introgression between different penguins species and their ancestors. From: Vianna et al. (2020) PNAS.


Vianna, J. et al. (2020). Genome-wide analyses reveal drivers of penguin diversification. Proceedings of the National Academy of Sciences117(36), 22303-22310.

Featured image: King Penguins (Aptenodytes patagonicus) © Ben Tubby | Wikimedia Commons

This paper has been added to the Sphenisciformes page.

2 thoughts on “Where did all these penguins come from?

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