March of the Fossil Penguins

Fossil penguin discoveries and research

Did Warham’s Penguin Survive into the 19th Century

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Warham’s penguin / Chatham Island crested penguin. Montage of skeletal elements. Chatham Islands. Image © Te Papa by Jean-Claude Stahl. From (click for original)

We recently introduced the extinct Warham’s Penguin, Eudyptes warhami. Our research team hypothesized this penguin was wiped out when humans arrived in the Chathams Archipelago over 700 years ago. There is good evidence for this, as some of the bones were found in middens (scrap heaps left behind at food preparation sites). So, we are sure that Moriori people encountered the penguins.

However, what if the penguins hung on until later colonists arrived?  The British ship HMS Chatham explored the archipelago in 1791. Captain William R. Broughton claimed possession of the islands for Great Britain – no matter than people had already been living there for centuries! Captain Broughton named the islands after the First Lord of the Admiralty, John Pitt, 2nd Earl of Chatham.

This “discovery” brought tragedy to the islands. Whalers and sealers began visiting the islands, bringing diseases. Then, in 1835 a group of nearly one thousand Māori arrived from mainland New Zealand. Soon after arriving they attacked the Moriori, killing hundreds and enslaving many of the survivors. Less than two hundred of the entire population of Moriori are believed to have survived.

By 1842, the Chatham Islands were officially annexed and made part of New Zealand and – long belatedly – the Moriori were released from slavery in 1863. By this time, Europeans had also established themselves on the islands and here we find an interesting written account of a penguin.

W.T.L. Travers read a paper to the Wellington Philosophical Society on September 11th, 1872, which is recorded in the Philosophical Transactions of the New Zealand Institute. In this paper, he reported on a number of birds collected on the Chatham Islands by his son, H.H. Travers. Many were specimens, but one was a penguin that was brought back alive. Travers (1872:221) reported: “I obtained and brought to New Zealand a live specimen of this bird, which had come ashore to moult”.

Today, no other species of crested penguins lives on the Chatham Islands, though several occur as occasionally as vagrants. Thus, Travers note about moulting is tantalizing. If the bird was moulting on the island, it may well have bred there as well. Perhaps Travers son had picked up one of the last Warham’s penguins in the world? We may never know, as the penguin is long dead and gone, and no photographs, feathers, or other remains seem to have been saved.

How did the penguin fare? Apparently it survived for several weeks without food while aboard the ship, but then took to eating fish and raw meat from the hands of its captures. By Travers  (1872:221) account, the bird became quite tame around humans but was a bully to the other birds in its pen: “Though generally considered stupid, no doubt from its appearance, it was extremely cunning. When placed at night in an enclosure with some poultry it became master of the situation, its harsh cry and powerful beak striking terror into the other occupants”.

So how does the fossil evidence come into play? So far it cannot provide conclusive evidence for the age of the last Warham’s penguin as we don’t really know if any of the skeletons found so far were from the last days of the species. But, some of the fossil bones were found in deposits mixed with items like glass beads, which would have only been available from the time Europeans visited onward. However, rabbit burrows have disturbed these deposits and so it is possible older bones and younger archeological items were jumbled up together.

Can this mystery ever be resolved? I certainly hope so. Radiocarbon dating could provide evidence that some of the bones of Eudyptes warhami date to more recent times. So far, none of yielded recent dates, but there are always more fossils to be discovered.


Written by Dan Ksepka

April 25, 2019 at 4:43 pm

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Dwarf Yellow Eyed Penguins

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On Tuesday, we met the recently extinct crested penguin Eudyptes warhami, discovered by a team studying subfossil penguin bones from the Chatham Islands. The study also turned up a “bonus” penguin. Some smaller bones collected at the sand dune sites were originally thought to belong to one of the smaller modern crested penguin species. However, mtDNA revealed something unexpected. The bones turned out to belong to a dwarf population of yellow-eyed penguin!

Flattened Megadyptes

Fossil bones of Megadyptes antipodes richdalei. Photos by Jean-Claude Stahl (Te Papa).

Yellow-eyed penguins are beautiful birds. They sport a yellow face mask, and as promised by their name have a bright yellow iris. It is easy to tell a yellow-eyed penguin skull from that of a crested penguin, due to the much more slender beak of the former. Yet, the rest of their bones are very similar and it is almost impossible to differentiate a large crested penguin from a yellow-eyed penguin based on the bones of the neck, flipper, or legs. Thus it is no wonder why the Chatham Island specimens were not identified immediately: the subfossil bones were so much smaller than the modern yellow-eyed penguins that the match seemed implausible.


A Yellow-Eyed Penguin, coming ashore in Dunedin, New Zealand. Photo by Daniel Ksepka.

Eudyptes warhami showed major DNA differences with living species, indicating it was a distinct species. Our team was also able to obtain intact mtDNA from the smaller bones. In this case they showed a very close relationship to modern yellow-eyed penguins. Indeed there were far fewer differences between the mtDNA sequences of the fossil and modern yellow-eyed penguins than between the fossil and modern crested penguins. Therefore, our team considered the smaller fossils to belong to a subspecies of the living Megadyptes antipodes, which we classified as Megadyptes antipodes richdalei, in honor of the late Dr. Lance Richdale, an expert on modern yellow-eyed penguins. While the concept of a subspecies is fairly messy, this recognizes that the Chatham Island dwarf penguins would have been easy to tell apart from their mainland relatives, but had not yet fully diverged genetically. Given a few hundred thousand more years, it seems likely that Megadyptes antipodes richdalei would have continued to evolve in isolation from its mainland relatives and eventually become a fully separate species.


Together, the crested penguin and yellow-eyed penguins of the Chatham Islands tell a complex tale of how species can be wiped out. Eudyptes warhami persisted for two million years only to be snuffed out in the blink of an eye. Megadyptes antipodes richdalei reveals a different kind of tragedy — it seems to have started on its way to becoming a distinct species, but had its evolutionary journey cut short before it had the chance.

Written by Dan Ksepka

February 8, 2019 at 12:10 pm

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Ancient DNA Reveals Lost Penguin Species

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Today, another species joins the March of the Fossil Penguins. We welcome Eudyptes warhami, an extinct crested penguin discovered on the Chatham Islands, an island archipelago about 500 miles east of mainland New Zealand.

Paleontologists have uncovered the remains of over 50 species of extinct penguins, most of them millions of years old. Eudyptes warhami is unique – it died out only a few hundred years ago, making it the youngest fossil penguin. Whereas most of the penguin species that have ever lived went extinct long before humans evolved, this species actually lived side by side with humans for a short time. Unfortunately, that brief encounter turned out to be deadly.


Composite fossil skull of Eudyptes warhami, an extinct penguin species from the Chatham Islands. Photo by Jean-Claude Stahl (Te Papa)

An international team of researchers extracted mitochondrial DNA from subfossil bones discovered in sand dunes on the Chatham Islands. I was fortunate to be a member of this team, which was led by Tess Cole, a PhD candidate at the University of Otago in New Zealand. Our study was published today in the journal Molecular Biology and Evolution. This project combined skeletal morphology with DNA evidence to understand how the new penguin evolved. Skeletal features provided the first clue – the existence of a lost species was hinted at by earlier comparisons of penguin bones collected from sand dunes on the Chatham Islands. Alan Tennyson (a co-author on the study) and Phillip Millener examined penguin bones from these islands, and found that they did not match up with those of any living species. DNA evidence has now confirmed those suspicions. Our team extracted mtDNA (a type of DNA that resides inside the mitochondria of cells and is inherited from the maternal line). We counted the number of nucleotide substitutions, a measure of how many mutations occurred since two species shared a common ancestor. The large number of substitutions between Eudyptes warhami and its closest living relative, Eudyptes sclateri (a living species known as the Erect-crested Penguin) confirmed that the subfossil bones belonged to a genetically distinct species. Our team named the new species Eudyptes warhami, in honor of Dr. John Warham, who carried out pioneering studies on crested penguins in New Zealand.

Comparisons of the bones to those of modern penguins, along with DNA evidence placing the penguin firmly within the crested penguin part of the evolutionary tree, allow us to get a clear picture of what it would have looked like. The beak was very deep like modern crested penguins, suggesting the new species was adapted to pursuing small prey including krill. Modern crested penguins have decorative yellow head plumes, and the evolutionary tree suggests Eudyptes warhami would have been no exception. Together with measurements, these details allowed Bruce Museum artist Sean Murtha to create a beautiful life reconstruction of the new species.

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Life reconstruction of Eudyptes warhami. Illustration by Sean Murtha.

Aside from the pristine bone preservation and intact DNA, another nice thing about new fossils is that they are young enough for carbon isotope dating. Carbon dating provides direct age estimates for organic material, but because of the relatively short half life of the radioactive isotope carbon 14, it cannot be applied to specimens that are more than 1 million years old. Carbon dates from the penguin fossils and associated remains of other birds suggest many of the specimens were only a few thousand years old. Indeed, some of the bones were found in piles of debris left behind at human cooking sites. This provides direct evidence that the Moriori, the first people to reach the Chathams, hunted Eudyptes warhami. The penguins appear to have been wiped out shortly after the Moriori arrived in the thirteenth century. How soon is a question that still remains unresolved, and will be revisited in future posts.

Though now lost, perhaps Eudyptes warhami can serve as a warning of the need for conservation efforts. For a long time, we thought penguins escaped the wave of human-driven extinctions that wiped out birds like the dodo, which disappeared in the seventeenth century, and the Great Auk, which became extinct in the mid-nineteenth century. Finding evidence that a crested penguin perished in the human era should remind us that we need to be even more careful with the species remaining under our stewardship.


Cole T. L. D. T. Ksepka, K.J. Mitchell, A.J.D. Tennyson, D.B. Thomas, H. Pan, G. Zhang, N.J. Rawlence, J.R. Wood, P. Bove, J.L. Bouzat, A. Cooper, S. Fiddaman, T. Hart, G. Miller, P.G. Ryan, L.D. Shepherd, J.M. Wilmshurst, J.M. Waters. 2019. Mitogenomes uncover extinct penguin taxa and reveal island formation as a key driver of speciation. Molecular Biology and Evolution.


Written by Dan Ksepka

February 5, 2019 at 7:46 pm

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A New Giant Penguin Weighs In

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March of the Fossil Penguins is gearing up for more penguin paleontology posts. We will start with a big story from the close of 2017. A new species, Kumimanu biceae, was discovered in New Zealand. The fantastic slippered fossil tipped the scales at 101kg (over 220lbs) and lived in the Paleocene Epoch, the first time period after the extinction of the dinosaurs. The team that discovered and studied the new species named it Kumimanu biceae. The genus name refers to it being a monstrous bird: “Kumi” is a Maori name for a huge sea monster whereas, and “manu” is the Maori word for bird. The species name “biceae” is based on “Bice”, the nickname of paleontologist Alan Tennyson’s mother Beatrice.


Top row: The broken humerus (main flipper bone) of Kumimanu compared to that of Pachydyptes (another extinct giant penguin) and Aptenodytes (emperor penguin). Bottom row: The coracoids of the same three species. Both of the fossil coracoids are broken. Photo courtesy of Dr. Gerald Mayr.

What makes the fossil really cool is is the combination of ancient age and giant size. We already knew that penguins appeared very soon after the extinction of the dinosaurs, as the oldest penguin fossils are about 62 million years old. And, we already knew giant penguins existed based on tremendous fossils such as Pachdyptes ponderosus and Kairuku waitaki. Kumimanu biceae pushes the jump to giant size in penguins right back near their origin. The new fossil is between 55 and 60 million years old and also of the largest on record. That is very interesting, because it means penguins ramped up to huge sizes very quickly after losing flight. They may have been able to balloon up to grand scales quickly because of a lack of competitors in the post-extinction world, after marine reptiles like mosasaurs andplesiosaurs vanished but before marine mammals like seals and sea lions had appeared.


Artist reconstruction of Kumimanu biceae with a human scuba diver for scale. Image courtesy Dr. Gerald Mayr.

Where does Kumimanu biceae rank on the scale of penguin size? It is hard to say precisely because many individuals are known only form a single bone, but the new species is likely the second largest penguin discovered so far. The humerus (main flipper bone) is not complete, but the intact portion is almost as big as that of Pachydyptes ponderosus, a contender for the title. It is clear there was quite a bit more to the humerus before it was broken, so we can rest assured it was larger overall. More importantly, the femur (thigh bone) is huge. While the femur of Pachydyptes ponderosus remains unknown, this giant femur shows that the penguin was huge overall rather than just having a long flipper. The one penguin that may have the edge on Kumimanu biceae is Palaeeudyptes klekowskii. A massive tarsometatarsus assigned to that species is the biggest on record and suggests it belonged to an even larger penguin. However, we can’t really be sure from just one bone as different species of penguins have different proportions (e.g., some have stouter legs and longer bodies, others have long flippers and small skulls, etc.). Regardless, we can be sure giant penguin prowled the waterways of the Southern Hemisphere for a very long time.

Written by Dan Ksepka

January 16, 2018 at 11:58 am

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Penguin Poop and Volcanic Ash: A Tale from Deception Island

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In celebration of World Penguin Day (April 25), let’s review a recent research paper on three exciting topics: penguins, poop, and volcanoes! A new paper by Dr. Stephen Roberts and colleagues reported a history of penguin colony collapses and revivals. Technically, there are no fossil penguins here: the populations studied only date back to 6,700 years ago. While ancient by human standards, this represents only 1/10,000th of the history of penguins as a group. And, the populations were studied not by looking at skeletons, but by looking at droppings!

The team studied guano (bird droppings) on Ardley Island. This small island sits near the tip of the Antarctic Peninsula and is a nesting site for many seabirds, including a thousands of Gentoo Penguins. As the penguins occupied the site, their droppings accumulated into guano layers. While guano may seem like merely an unfortunate byproduct of penguin digestion, it is serious business. Guano has long bee used as fertilizer, and been the subject of treaties, territorial disputes, and even wars. The Guano Islands Act of 1856 basically claimed all unoccupied guano-bearing islands in the oceans for the United States. Peru and Chile even fought a “Guano War” (also known as the Chincha Islands War) over disputed guano-rich islands.

Guano is also a useful substance for scientists, as the ratios of different isotopes can reveal how long ago a guano layer formed and what the animals that made it might have been eating. The amount of guano that forms per year also gives an estimate of how many penguins were “contributing”. In this study, scientists found evidence that penguin populations on Ardley Island had crashed precipitously several times in the past. The culprit? A volcano. Roughly 60 miles to the southwest lies Deception Island. The volcano that created this island has erupted periodically over the past few thousand years.


Deception Island. Photo by Christopher Michel.

By looking at carbon isotope levels in plants, bone, and sediments from guano layers, the team was able to estimate the age of each layer and tie the penguin poop peaks and crashes into the timeline of local events. At least three times, the belching eruptions of the Deception Island volcano wiped out the penguin colony. Because no skeletons from the time of the volcanic eruptions remain intact, the fate of the penguins living in the area in the days of the eruptions is uncertain. Falling ash may have wiped out nesting adults and chicks, buried eggs, or spoiled food sources. It is also possible the effects did not wipe out the full grown penguins, but instead forced them to flee their breeding colony leaving an abandoned landscape of rocky shores.

Nevertheless, the penguins ultimately prevailed. After each eruption, the penguins slowly returned, typically taking 400-800 years to regain their original population levels. Today, thousands of penguins are happily inhabiting the island  (and building up that guano layer bit by bit).


Gentoo Penguin chicks on present-day Ardley Island. Photo by Henrike Mühlichen



Roberts, S. and Monien, P. and Foster, L. and Loftfield, J. and Hocking, E. and Schnetger, B. and Pearson, E. and Juggins, S. and Fretwell, P. and Ireland, L. and Ochyra, R. and Howarth, A. and Allen, C. and Moreton, S. and Davies, S. and Brumsack, H. and Bentley, M.J. and Hodgson, D. (2017) ‘Past penguin colony responses to explosive volcanism on the Antarctic Peninsula.’, Nature communications. .


Written by Dan Ksepka

April 25, 2017 at 10:55 am

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An Hour of Code with Penguins

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As we mentioned last post, March of the Fossil Penguins will be covering some exciting new research over the next three years. I’m very fortunate to be involved in a new project working with Dr. Tracy Heath and Dr. Rob Meredith. One of the main goals of the grant is to develop more sophisticated computer models to reconstruct evolutionary trees that include both living and fossil species. We chose penguins as one of our “test cases”, because they have a rich fossil record with lots of specimens and well-constrained geological dates.


Kate Dzikiewicz explains how code can be used to create an electronic penguin adventure to a school group.

We are excited about sharing our results with the public, and helping build computer literacy is one of our major outreach goals. As part of the project, the Bruce Museum’s amazing Paul Griswold Howes Fellow, Kate Dzikiewicz, has been hitting the road to bring an Hour of Code to hundreds of students.  Computer coding is one of the most widely useful skills students can learn, as basic coding abilities can be used in careers ranging from the biological sciences to graphic design. Hour of Code is a global initiative that aims to bring an hour of computer coding lessons to as many students as possible, and we are putting our own spin on it, with a little help from a new virtual friend named Kari the Kairuku penguin.


Kate created Kari to make coding more fun. She is based on an ancient penguin who lived in New Zealand  27 million years ago, and reached a height about a foot and a half taller than an Emperor Penguin. Kids learn techniques for guiding Kari’s movements, looping actions, adding animations and more. Then, they can turn their imaginations loose and code up their own adventure for Kari.

Check out the story of Kari here:

Written by Dan Ksepka

March 28, 2017 at 11:26 am

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A New Look at the Penguin Evolutionary Tree

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This week, a new study of the penguin evolutionary tree officially appeared in Systematic Biology (though the proof has been available online ahead of formal publication). This represents the first paper from an exciting new project aiming to develop Bayesian methods for combining data from fossils and living species. I’ll be teaming with the exceptional duo of Dr. Tracy Heath of Iowa State University and Dr. Rob Meredith of Montclair State University on this project, and penguins will be one of the “test pilot” groups to try out the new methods.

Our first foray into this realm was to re-analyses a dataset that was originally developed for a parsimony analysis of the giant fossil penguin Kairuku in 2012. This dataset includes 245 morphological characters and >6000 molecular characters. Our re-appraisal was led by PhD student Sasha Gavryushkina of Auckland University. We applied the Fossilized Birth-Death Process, a model pioneered by Dr. Heath that explicitly acknowledges that extant species and fossils are representatives of the same macroevolutionary process, in a tip-dating framework which allows fossil ages to be incorporated into the tree directly. Our analyses thus allow the ages of the fossils to directly impact the shape of the tree, and in a new wrinkle also allow for the possibility that some fossils species may be ancestors to one or more other species.

The results are shown below. One pattern that emerges immediately is that penguins are a very old group, extending back past 60 million years, but that crown penguins only started radiating between 13 and 14 million years ago. Thus, we have evidence for a recent wholesale replacement of “primitive” penguins by “modern” forms. Our work also benefits from some recent geological work, which for example has shown that Spheniscus muizoni, a fossil penguin thought to be 11-13 million years old, is actually close to 9 million years in age. In one reversal of previous findings, the fossil penguin Madrynornis mirandus is pulled outside the EudyptesMegadyptes clade in our study.


To me, the most intriguing message comes from the dates: modern penguins are young. Our dates are much younger that those recovered by past studies that looked only at DNA from living penguins. Adding the fossil data has a major effect, and it is very important: because about 3/4 of all known penguin species are now extinct, ignoring the fossils is like looking at just one small piece of a large puzzle. Our new dates place the origin of modern penguins at a really interesting time in Earth history: the Middle Miocene Transition. This transition marks the start of a global shift from warmer to cooler climates that ultimately leads to the glacial-interglacial cycles of our modern world. The accompanying expansion of Antarctic ice sheets may have opened up new habitats for penguins.  In deed, we find that the peaking of glacial advance-retreat cycles in the Pleistocene may have been a driver of penguin evolution: 12 of the 18 living species likely arose in the last 2 million years according to our results.

Over the next three years, our team will be working on improving these methods and expanding their capacity to incorporate other types of data, such as the geographic locations of fossils and how frequently fossils occur within their overall stratigraphic ranges.



Gavryushkina, A., T.A. Heath, D.T. Ksepka, T. Stadler, D. Welch, and A.J. Drummond. 2017. Bayesian total evidence dating reveals the recent crown radiation of penguins. Systematic Biology 66 (1): 57-73.

Written by Dan Ksepka

March 13, 2017 at 11:23 am

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