Paleontology in a Sink Hole: Spring Break Edition

Last week, I spent time at the Bahamas Natural History Symposium in Nassau, Bahamas. Seeing policy makers, ecologists, educators, geologists, and anthropologists come together was awesomely inspiring for the future of The Bahamas, a wonderful place with a magnificent natural environment! If you are fossil hunting ,The Bahamas might not immediately come to mind as a paleontological destination, but you would be wrong! The Bahamas is a large carbonate platform that may have started forming as early as the Cretaceous. The carbonate rock was exposed to the air during the Pleistocene, and during this time sand dunes lithified and formed the islands. During the last glacial maximum, the Bahamas bank was exposed greatly increasing the landmass and connectivity of the Caribbean, fostering biotic interchange between the islands. Now this shelf is submerged again so the islands remain isolated. The limestone that the islands are based on is porous and can be dissolved, so during glacial maxima, weathering of this limestone lead to features that make these islands so special today—underground caves, sink holes, and pits.

The Bahamas. The light blue shallow water is the carbonate shelf that was once exposed during the Last Glacial Maximum. From NASA on Wikimedia Commons

When sink holes and caves fill with water, these underground networks become submerged ethereal mazes that preserve unique life forms. Besides looking beautiful, blue holes as they are called, become a quiet resting place for anything –animal or human—that might end up in there. The blue holes of Abaco in The Bahamas have preserved a rich paleontological and anthropological history spanning thousands of years. On Great Abaco Island, there are a few of these astonishing features, but especially notable is Sawmill Sink. Sawmill Sink, one of the most famous blue holes in The Bahamas, contains the bones of numerous vertebrates that no longer live on the islands or are completely extinct. It is a spectacularly preserved graveyard of tortoises, birds, and crocodiles. Even human bones have found in Sawmill Sink, a remnant of the original prehistoric inhabitants of The Bahamas, the Lucayan people. Since these underwater caves were not always filled with water—as I previously mentioned, sea level was lower—the Lucayans were able to bury individuals in these limestone caves. The bones in the cave are perfectly preserved and also contain organic collagen, so they can be dated using carbon-14. The human remains in Sawmill Sink date from 1050 to 920 calendar years before present, making this the earliest evidence of human inhabitance of the Bahamian Archipelago.


Dean’s Blue Hole in Long Island, The Bahamas. By Ton Engwirda Wikimedia Commons

Up to 54 individual crocodile specimens have been found in Sawmill Sink that are dated to 2780 years before present, predating any human occupation of The Bahamas. The species of crocodile is Crocodylus rhombifer, the Cuban crocodile. There are currently no crocodiles in The Bahamas, and the Cuban crocodile is limited only to a very small region of Cuba. How the Cuban crocodiles found in Sawmill Sink are genetically related to the current Cuban population remains unknown, but it is quite possible ancient DNA can be obtained from the well preserved specimens. Additionally, why did they go extinct from most of the West Indies? It is supposed that the extinction was caused by human encroachment and hunting, which make sense, because C. rhombifer bones are found in archaeological middens, along with other extinct tortoises that would have been a tasty meal, throughout the islands of The Bahamas.

Cuban crocodile in a Miami zoo. By Alexf Wikimedia Commons

Cuban crocodile in a Miami zoo. By Alexf Wikimedia Commons

Birds, such as the now extinct Bahamas caracara, and the Bermuda petrel (now only in Bermuda) are found preserved in blue holes indicating the avifauna of the Caribbean was once very different and perhaps a lot more diverse. These fossil deposits preserve a unique time in geological history when both humans and large vertebrates were inhabiting space-limited environments. Detailed study of these fossils can potentially help us see at a fine-scale the impact human settlement can have on biodiversity. Since blue holes are so spectacular, there are a myriad of great photographs out there, specifically through National Geographic. I suggest you take a look because the images are just fantastic.

Now if you’ll excuse me I am off to spring break. Paleontologists need some beach time too!

Additional reading:

Morgan, G.S. and N. A. Albury. 2013. The Cuban crocodile (Crocodylus rhombifer) from the Late Quaternary fossil deposit in The Bahamas and Cayman Islands. Bulletin of the Florida Museum of Natural History 52(3): 161-236.


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Shake Your Tail Bone! (and shape your skeleton, if you’re a bird)

This is either a cheap tactic to increase blog traffic via cats, or an oddly relevant image. The Manx cat has a mutation that results in a shortened tail.

This is either a cheap tactic to increase blog traffic via the internet’s unhealthy obsession with cats, or an oddly relevant image. The Manx cat has a mutation that results in a shortened tail. Image by Karen Slemmer, CC-BY.

Those poor tail bones, always getting shortened and lost during the course of evolution. A long tail is the default condition for four-limbed vertebrates, but this tail disappears with shocking regularity. Frogs ditched theirs early in their evolutionary history. Humans and other apes did the same. And, of course, birds.

Well, perhaps disappear isn’t quite the right word for what happened in these groups. The tail is still there–just with many fewer vertebrae. Those of us who have carved up a turkey or chicken don’t pay much attention to their pitiful tails. It’s a fatty little nub, without much in the way of meat, bound for making soup stock. If you’re weird like me (when I was 12 or so, I cleaned and mounted the bones of our Thanksgiving turkey), you might have picked apart the tail and noticed a few things. First, the bones are pretty simple…most of the vertebrae behind the hip are short and squat. But most intriguingly, the last little chunk of tail is particularly weird: a flattened mass of bones, formed from several vertebrae fused together. The technical term for this structure is a pygostyle.

Peregrine Pygostyle.

Skeleton of a peregrine falcon–the bone highlighted in green is the pygostyle. Image from Eyton 1867, in the public domain.

Even though the pygostyle is a pitiful-looking bone, it (and its surrounding tissues) are important for anchoring the spectacular tail feathers of many birds. In turn, these tail feathers are shaped in part by how birds use these tails–whether in slow soaring flight, rapid plunges through the air, or long aquatic dives in pursuit of fish. A close relationship between the anatomy of the wing bones and locomotion style has been documented in many bird groups–after all, the wings are the obvious system to investigate for birds. But do the same relationships between locomotion and bony anatomy apply to the tail?

Ryan Felice, a Ph.D. student at Ohio University, and Pat O’Connor, Ryan’s graduate advisor, documented shapes and sizes for the loose tail vertebrae and pygostyles from 51 species representing a variety of waterbirds and shorebirds. The sample included everything from loons to penguins to storks to seagulls, spanning a variety of body sizes and locomotion styles. So, what did the researchers find?

It turns out that pygostyle shape is closely related to foraging style–birds that forage underwater, such as penguins, have a shape that is quite different from that seen in birds that forage from the air. And similar shapes appear convergently in evolutionarily distant lineages. Penguins, puffins, and boobies are separated by at least 60 million years of evolution, but all have a long and straight pygostyle. They also all chase after their prey underwater.

What a long and straight pygostyle you have there, Penguin. Then again, I say that to all of the underwater foragers. Image by LoKiLeCh, CC-BY.

What a long and straight pygostyle you have there, Penguin. Don’t feel special, though. I say that to all of the underwater foragers. Image by LoKiLeCh, CC-BY.

So why these convergences? Felice and O’Connor suggest that underwater locomotion has a unique set of demands on the skeleton from aerial locomotion, perhaps related to particular patterns of muscle development or to resist forces applied to the skeleton when using the tail as an underwater rudder. Or, it might have something to do with the orientation of the tail feathers in diving birds (more research is required on this latter point).

The new study, published last week in PLoS ONE, documents yet another way that bird skeletons reflect their lifestyles. From a paleontological perspective, the work will hopefully open another path to infer the behavior of fossil species. So the next time you see that pygostyle on a bird, make sure to say thank you for being such a nifty feature!

Want to learn more? Read the paper in PLoS ONE!
Felice RN, O’Connor PM (2014) Ecology and caudal skeletal morphology in birds: the convergent evolution of pygostyle shape in underwater foraging taxa. PLoS ONE 9(2): e89737. doi:10.1371/journal.pone.0089

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The asteroid started the fire (or did it?)

Poor guys didn’t know what hit em. Public Domain via Wikimedia Commons by Donald E. Davis

In December, I listened to the Radiolab “Apocolyptical” show which was all about the Cretaceous-Paleogene boundary event. Famously, in 1980, Walter Alvarez and colleagues described an iridium anomaly at the K/Pg (also known at K/T) boundary which was subsequently specifically tied to an extraterrestrial impact event. The crater from this impact is around 200-km wide off the coast of the Yucatán in Mexico, known at the Chicxulub Crater.

But what happens when a 10 km (6 mile) wide rock smashes into Earth’s surface? When this object made impact, hot, melted rock was ejected and these little rock balls (spherules) rained down and can be found in deposits of K/Pg age rocks worldwide. There is little debate that this enormous disruption to the entire Earth was responsible for the large-scale extinction we see at the K/Pg boundary. But what, more specifically, did the molten rock and rock vapor have to do with it?

Back to the Radiolab. I was surprised as I listened to it that the hosts were taking an angle of “everything you have learned about dinosaur extinctions is wrong!” From my own experience, it is taught that the final nail in the coffin for dinosaurs, plants, and other animals was a long-lasting “impact winter.” The amount of debris kicked up into the atmosphere would have been so extreme, it would have blocked out the sun, reduced photosynthesis, and caused a cooling period. This cooling period, although it probably only lasted about 2,000 years, would be devastating to ecosystems worldwide. I don’t think there is much doubt an impact winter actually happened, but the stance this radio show took was that this was absolutely not the cause of the massive vertebrate extinction.

Their source on this was work done last year, mainly through computer modeling, that calculated the infrared (IR) radiation heat pulse and subsequent probability of global wildfires caused by molten ejecta re-entering the atmosphere. Douglas Robertson published a comprehensive review of the heat-fire hypothesis, noting that by calculating the kinetic energy converted to IR radiation by ejecta re-entering the atmosphere, a temperature could be reached on the surface of the Earth that is sufficient to ignite plant matter and tinder, causing global wildfires.

Much of this review is dedicated to addressing the problems with this hypothesis raised by other researchers. This often comes down to the morphology and fine structure of the soot found in K/Pg age rocks. While proponents of the heat-fire hypothesis say that soot found is clearly from widespread forest fires, the research of scientists like Claire Belcher suggests otherwise. Her research indicates that these soot deposits are not soot from the burning of plant matter, but actually hydrocarbon combustion from the impact site. Additionally, she puts forth compelling evidence that while there would have been IR radiation coming from the spherules, it mainly would have been shielded from the Earth by the spherules actually settling and forming a cloud in the atmosphere. The spherules’ interaction with the atmosphere potentially prevented the surface of the Earth from being completely incinerated. Of course, the other camp argues the charcoal deposits have signs of coming from ignition of plants and not of hydrocarbons. The debate rages on.

So was every living thing not underground or in the water burned up almost immediately by an IR radiation pulse? Or was there not truly enough heat reaching the Earth’s surface to cause such widespread fire, and extinction was driven mainly by other factors such as acid rain or impact winter? It is hard to know if we will ever be 100% certain, but I find the debate fascinating. Do I think it is right to tell the public everything the know about the dinosaur extinction is wrong? Honestly, I don’t think it is the best way to go about things, because there is still so much debate on this topic and scientists have not reached a consensus, and may never have a unified theory. What do you think about this debate? Any strong opinions either way? If you are an educator, what do you teach your students?

Photo representation of what the non-avian dinosaur extinction may have looked like

Photo representation of what the non-avian dinosaur extinction may have looked like

Category: Climate Change, Dinosaurs, Paleontology | Tagged , , , | 5 Comments

Did Dinosaurs Enjoy Chocolate?

Dinosaurs dining on a chocolate kiss - image (c) Emily Willoughby, used with permission.

Dinosaurs dining on a chocolate kiss…did they ever encounter a cocoa bean? – image (c) Emily Willoughby, used with permission.

Every living thing has a remarkable evolutionary history, stretching back through the eons. Sometimes it’s fun to think about common plants and animals alongside the dinosaurs of the Mesozoic–particularly when there is a fossil record to match! For instance, ancient relatives of ginger are pretty common in the fossil record, so Triceratops might have enjoyed a good herbal tea, and giant Jurassic sauropods could have been serenaded by chirping katydids. But, it’s Valentine’s Day, so I want to know: Did Velociraptor (or its cousin Deinonychus, shown above) trade boxes of chocolates?

That’s obviously a frivolous question, so let’s rephrase it in paleontological terms…was chocolate (or at least its source plant) around with the dinosaurs? To investigate that, we need to delve into the fossil record.

Chocolate is made from the cocoa bean, which is the seed from the fleshy fruit of the cacao tree (Theobroma cacao). The cacao tree is part of a group of plants called the Byttnerioideae, which in term belong to a group called Malvaceae. We could go on and on from there, but suffice to say they are angiosperms, or flowering plants. So, do cacao trees or any of their relatives show up in the fossil record?

Cocoa pods on the tree. Image by medicaster (public domain).

Cocoa pods on the tree. Image by medicaster (public domain).

An alleged fossil cocoa pod–named Theobroma fossilium [PDF of the original description]–was found in rocks of uncertain age in Colombia (dated to sometime in the last 65 million years), but it later turned out to be part of a fossil jaw [paywalled article]! So, that’s a bit of a dead end.

Byttnerioideae, the group of plants most immediately including the cacao tree, has a pretty dismal (i.e., virtually nonexistent) fossil record. Estimates from molecular clocks (based on gene sequences of modern plants) suggest the group split from other plants between 36 and 20 million years ago–well after the non-avian dinosaurs went extinct! The fossil record for the Malvaceae (the group containing Byttnerioideae and their relatives) is a little better, with possible wood known from around 75 million year old sediments in Texas, and some leaves from around the same time. If you’re interested in a detailed account of fossil Malvaceae, there is a nice summary in a recent paper by Carvalho and colleagues.

The short version of all of this is that only the most distant relatives of cocoa beans grew alongside Velociraptor and friends. But, the news isn’t so bad for every prehistoric animal, especially those from the last million years. Some researchers speculate that giant ground sloths and gomphotheres (elephant relatives) feasted on big fruits like those from the cacao tree. So, even if our beloved dinosaurs never enjoyed chocolate, we can be comforted by the fact that cocoa beans may have passed through a ground sloth butt sometime in the Pleistocene.

Painting by Heinrich Harder, in the public domain.

Poor Megatherium, stuck eating raw cocoa pods. No chocolate kisses for this ground sloth. Painting by Heinrich Harder, in the public domain.

A big thank you to scientific illustrator Emily Willoughby, for letting use her artwork for this post. Be sure to check out her website for more gorgeous renderings!

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Turtles Lost and Turtles Found

Science is built upon repeatability, but this means different things in different fields. For instance, a chemist in one lab should be able to follow the procedures of another lab and get the same results. In a historical science like paleontology, repeatability depends in part upon being able to restudy previously published fossils in order to verify and expand upon previous observations. Nowadays, museums are the custodians of these irreplaceable specimens. But what happens when a fossil goes missing?


With the originals lost in the chaos of World War 2, replicas are all that remain of the Homo erectus fossils known as ”Peking Man.” Image by José-Manuel Benito Álvarez (public domain).

Sadly, the disappearance of fossils is not totally unheard of. This can happen in wartime (as in the case of the sail-backed dinosaur Spinosaurus or with the fossils of “Peking Man”), by outright theft, or if a privately owned fossil was published upon and then later lost after the death of the owner. The published descriptions remain, of course, but they cannot be verified (e.g., if there is a question on what is reconstructed versus what is real bone), nor can the fossil be reprepared or restudied using “modern” techniques (such as CT scans, geochemistry, or histology). Science always suffers as a result.

Sometimes, paleontologists get a second chance. Let’s follow the twisted tale of a Jurassic turtle for one such case.

Way back in 1857–two years before Charles Darwin published On the Origin of Species–Swiss paleontologists François Jules Pictet de la Rive and Aloïs Humbert named a new species of extinct turtleEmys etalloni. The fossil consisted of a shell (carapace and plastron, in the technical terminology) collected in the Jura Mountains of eastern France, from rocks now dated to around 150 million years old. That much is straightforward, but from here the story gets tangled up in church politics.

The shell of Emys etalloni in side view (from Pictet and Humbert 1857)

The shell of Emys etalloni in side view (from Pictet and Humbert 1857)

The fossil of Emys etalloni was collected by a French priest, who passed it along to another priest (in fact, the vicar general of the Saint-Claude diocese, Joseph Célestin Girod), who in turn let paleontologists Pictet and Humbert study the fossil. Girod’s superior, Bishop Mabile, helpfully offered to turn the fossil over to a local scientific society, and from there the specimen briefly ended up in the Natural History Museum of Besançon. This apparently didn’t please Vicar Girod, because he claimed that he never agreed to part ownership with the specimen. As a result, the fossil was returned to Girod, and then lost to the mists of history after he passed into the great beyond in 1863.

The original description remained in the scientific literature, and a few plaster replicas of variable quality were scattered across museums in France and Switzerland. Emys etalloni was later moved into the genus Plesiochelys, but any rigorous study of the original fossil was severely limited. This was particularly problematic, because the identity and relationships of Jurassic-aged turtles from Europe are on the messy side. Depending upon which article you read, Plesiochelys etalloni was the same as some other species or its own species. In fact, up to six other turtle species had been lumped in with P. etalloni. Some more recently discovered fossils were assigned to P. etalloni outright, too. But, were they all really the same thing as the lost French turtle? Subtle textures and markings on the shell that were necessary to resolve the issue couldn’t be confirmed from the published illustrations, and plaster replicas didn’t help either. In the end, the real fossil was needed to settle the score.

The problem has particular relevance to paleontologists because turtles like Plesiochelys branched off near the origin of modern cryptodire turtles (the most common group of turtles, including everything from your typical pond turtle to the giant Galapagos tortoises), and are thus important for tracing turtle evolution. Although more recently discovered fossils in some ways made up for the missing fossil, which name went to which fossil was pretty nebulous. There was no way to know for sure without the original fossil of Plesiochelys etalloni!

In the worst case, perhaps the fossil shell had been thrown away after Vicar Girod’s death (after all, a heavy rock isn’t the most logical thing to keep). Somewhat miraculously, this wasn’t the case. It turned out that Vicar Girod sold the fossil to a collector, and the fossil stayed in this collector’s family for over 100 years. Perhaps wanting to properly dispose of a weighty heirloom (we can speculate), the family donated their inheritance to Musée d’archéologie du Jura in Lons-le-Saunier, France, back in 1994. Twenty years later, paleontologists Jérémy Anquetin​, Sylvie Deschamps, and Julien Claude recognized the specimen in the museum collection. Finally, they were able to redescribe the fossil in a recently published article in the open access journal PeerJ [full disclosure: I was the editor who handled their paper].

Top (A) and bottom (B) views of the turtle shell.

Top (A) and bottom (B) views of the shell of Plesiochelys etalloni. From Anquetin et al. (2014), CC-BY.

With the fossil in hand, Anquetin and colleagues answered some long-standing questions about Plesiochelys etalloni–most importantly, confirming its distinct identity. Of course, a thorough redescription and refiguring of the specimen led the way. Scientists who can’t visit the specimen in person now benefit from clear color figures and measurements. On top of this, the research team verified that at least three other previously named species (P. langii, P. sanctaeverenae, and P. solodurensis) were the same thing as P. etalloni. This is a critical finding, because specimens of these other “species” had skulls with them, which the recently rediscovered turtle did not. Skulls are important for unraveling fossil turtle relationships and behavior, so being able to more confidently match skulls and shells across the board is really nice!

Skull of Plesiochelys etalloni, from a specimen discovered in 1950 in Switzerland. Modified from Carabajal et al. 2013, CC-BY.

Digital reconstruction of the skull of Plesiochelys etalloni, from a specimen discovered in 1950 in Switzerland. Modified from Carabajal et al. 2013, CC-BY.

From the seas of the Jurassic to the ecclesiastical politics of 19th century France to the digital pages of 21st century journals, Plesiochelys has quite a story to tell. With its original fossil safely (and hopefully permanently) in a museum, the next chapter finally can be written.

Anquetin J, Deschamps S, Claude J. 2014. The rediscovery and redescription of the holotype of the Late Jurassic turtle Plesiochelys etalloni. PeerJ 2:e258

Carabajal AP, Sterli J, Müller J, Hilger A. 2013. Neuroanatomy of the Marine Jurassic Turtle Plesiochelys etalloni (Testudinata, Plesiochelyidae). PLoS ONE 8(7): e69264. doi:10.1371/journal.pone.0069264

Pictet F-J, Humbert A. 1857. Description d’une émyde nouvelle (Emys etalloni) du terrain jurassique supérieur des environs de St-Claude. In: Pictet F-J, ed. Matériaux pour la paléontologie suisse. Première série. Genève: J. Kessmann. 1-10 [freely available via Google Books]

Above: 3D scan of Plesiochelys etalloni, from Anquetin et al. 2014. CC-BY.

Category: Museums, Paleontology | Tagged , , , , | 2 Comments

Rodents of the Caribbean: The Curse of the Quaternary Extinction

The Caribbean is typically thought of as a lovely spring break destination. If you are an animal lover, the area is great for diving and birding, but there are not many land mammals to be found. Sure, you will find bats, some endemic rodents, and of course invasive cats and rats, but besides that you will not find anything larger, like, oh, a sloth.

Where's my piña colada? Public Domain- Wikimedia Commons

Where’s my piña colada?
Public Domain- Wikimedia Commons

That’s right, up until a few thousand years ago, sloths weren’t just a South American thing. There were also primates, specifically New World monkeys like the Jamaican monkey, on islands throughout the Greater Antilles. The Greater Antilles consist of Cuba, Hispaniola, Puerto Rico, Cayman Islands, and Jamaica.

Map of the Greater Antilles in green. Other Caribbean islands like the Bahamas and Turks and Caicos have had mammalian extinctions Wikimedia Commons

Map of the Greater Antilles highlighted in green. Other Caribbean islands like the Bahamas and Turks and Caicos have also had mammalian extinctions
Wikimedia Commons

This now extinct terrestrial fauna of the Greater Antilles still remains very mysterious for a variety of reasons. As previously mentioned, only a few species of endemic rodents remain on Caribbean islands. The two biggest questions in this evolutionary conundrum are how did the mammals arrive? And then, how did they go extinct? The arrival debate is probably the most contentious- if we know the ancestors of extinct Antillean sloths, primates, and rodents originated in South America, how did the end up on islands in the middle of the Caribbean Sea? Did they all come from South America? It is possible, but seemingly unlikely, these different groups of mammals came in a series of overwater dispersals. A sloth floating its way to Jamaica may seem unbelievable, but overwater dispersals can be viable migration methods.

There is another theory though—perhaps there was a late Eocene- early Oligocene land bridge that connected the Greater Antillean Ridge and South America via the Aves Ridge. Welcome to:


GAARlandia was proposed by Iturralde-Vincent and MacPhee in 1999 as a way to explain the dispersal of land mammals from South America to the Caribbean islands in one continuous event, rather than a series of random overwater dispersals. Phylogenetic evidence has both supported and refuted the potential for the existence of GAARlandia, so the debate can still continue.

This month, in the Journal of Vertebrate Paleotology, Vélez-Juarbe et al. describe rodent incisors from Puerto Rico that date to the Oligocene- making them the earliest rodent fossils in the Caribbean. They are just incisors, so we cannot learn too much about the actual animal they belonged to (besides the fact their enamel structure indicates they belonged to a caviomorph rodent), but the existence of this fossil pushes back the date of rodent arrival in the Greater Antilles by approximately 9 million years. This new date is consistent with other molecular divergence estimations of caviomorph rodent groups in South America. In addition, a dated molecular phylogeny indicates there was a split between a Greater Antillean toad and its sister taxon in South America during the late Eocene- early Oligocene.  The coincidence between molecular divergence dates, paleontological finds, and the hypothesized date of the land-bridge adds support to the idea there may have been a short lived sub-aerial land bridge bringing non-flying mammals to the Greater Antilles.  Of course, this new evidence still does not preclude the possibility of overwater dispersal! These biogeographic hypotheses are very difficult to disprove so the debate rages on.

So where have the Caribbean monkeys and sloths gone? The Caribbean mammalian fauna experienced extremely high rates of extinction during the Quaternary, and these extinctions seemed to occur both before and after humans were a factor in the environments. During the Holocene, climate change could have potentially altered the environments these mammals were living in and this caused their extinction. But with the arrival of humans, overhunting, habitat destruction, disease, and introduction of invasive predators could also have been extremely damaging to biodiversity. The zooarchaeological and paleontological records on these islands can be spotty, but much more remains to be done to figure out the complex history of the ancient life of the Caribbean. Ancient DNA, stable isotopes, and re-examination of the taxonomy of fossils and sub-fossils from the Caribbean will continue to inform biogeographic theory and help us understand what drove such a unique mammalian biota to extinction.


Iturralde-Vincent, M. A., R. MacPhee. 1999. Paleogeography of the Caribbean region: implications for Cenozoic biogeography. Bulletin of the American Museum of Natural History 238:1-95.

Velez-Juarbe, J., T. Martin, R. D. E. MacPhee, D. Ortega-Ariza. 2014. The earliest Caribbean rodents: Oligocene caviomorphs from Puerto Rico. Journal of Vertebrate Paleontology 34:157-163.

Category: Geology, Paleontology | Tagged , , , , | 3 Comments

Paleo Podcasts

When I work out, I sometimes listen to a mix of aggressive electronica and high-energy dance music to get me moving. But usually, I use my gym time to catch up on podcasts. My new year’s fitness resolutions mean I’ve been updating my mp3 player with new podcasts, including some paleontology-themed ones. The problem is, when you go to iTunes and search “paleontology”, “palaeontology”, or even “dinosaurs”, you don’t get much. Here are a few for the paleo-minded.

I’ll begin with a plug for my peeps: Past Time is hosted by Stony Brook University grad students Adam Pritchard and Matt Borths. Every couple weeks they post a ~20-25 minute show on some topic relating to vertebrate paleontology, and despite the hominid focus at Stony Brook, it’s rarely about humans. In addition to their entertaining and informative banter (Adam is a perfect straight man to Matt’s charming goofiness), each episode includes an interview with a paleontologist who worked on the topic of discussion. For example, recently they chatted about all these new tyrannosaur species discovered by University of Utah scientists, with Utah professor Dr. Randy Irmis as a guest. The interviews are woven into the discussion on the topic rather than longform interviews. One really awesome feature of Past Time is that they create a “field guide” for each episode, an associated page with tons more information, photos, maps, and further reading, including links to the original scientific papers (here’s the tyrannosaur field guide). The most recent episode is “The Hobbit – An Unexpected Discovery“, which discusses the species of tiny hominids living in Indonesia just 17,000 years ago, Homo floresiensis. This show is definitely kid-friendly (no swearing, shorter), and it’s accessible to non-scientists in language/themes).

For more Past Time, head to their website, subscribe on iTunes, and follow them on Twitter and Facebook.

You should also check out Palaeocast, a UK show hosted by Dave MarshallLaura Soul, Joe Keating, and Jon Tennant. This show is a bit longer, 30-60 minutes per episode, with a new ep every two weeks. It’s a different style than Past Time; the interviewees are the focus and they have a longer chance to explain their research. Some recent shows I liked are a general overview of marsupial evolution and a discussion of the Riversleigh fauna, both featuring Dr. Robin Beck from the University of New South Wales. Another rad aspect of Palaeocast is that they cover scientific meetings; for example, these recent eps on the Society of Vertebrate Paleontology and the Palaeontological Association annual meetings. The pages for each podcast are image-rich, with pictures from the meetings or from the scientific papers the interviewee discusses. You could play this podcast with your kids in the car (no swearing), but younger kids with short attention spans might not like the longform interviews. Adults, however, will appreciate the clarity and depth of the discussions.

For more Palaeocast, head to their website, subscribe on iTunes, and follow them on Twitter. You can also like them on Facebook.

paleo after dark

Palaeo After Dark features ”informal discussions about evolutionary biology and palaeontology… over beer”, and is hosted by four current or recent University of Kansas geology graduate students: Curtis Congreve, Amanda Falk, James Lamsdell, and Randol Wehrbein. This is also a biweekly podcast, and it’s easily the longest of the bunch (some episodes are close to two hours). This podcast is stylistically a lot different from the ones above; it’s four friends discussing topics relevant to their shared research interests or primary literature. It’s neat to get this perspective into how academics interact with each other; this is far closer to how most science conversations start than the stodgy, formal, or awkward stereotype you see in movies or Big Bang Theory. Palaeo After Dark assumes their listeners are already pretty familiar with paleontological and evolutionary terminology, so it might not be as accessible to nonscientists. It also usually takes a long time to get to the meat of the episode. For example, the gang has over 26 minutes of amusing banter before they begin this interesting discussion of dinosaur ontogeny, taxonomy, and geologic dating. Because this is an informal podcast and alcohol is involved, there is a lot of swearing, so it’s probably not kid-appropriate.

For more Palaeo After Dark, head to the website, subscribe on iTunes, and like them on Facebook.

Dragon Tongues paleontology podcast

Our final paleo-exclusive podcast is Dragon Tongues, a show so new its first episode just aired on January 7th. Hosted by Sean Willett (an undergrad! at University of Calgary who also writes a dino column for UBC Okanagan’s The Phoenix News), Dragon Tongues will air the first Wednesday every month. It’s pretty short if the first episode (15 minutes) is a good indication. The first show begins with a statement of purpose: Sean’s goal is to tell the stories of fossils and Earth history in an accessible format, with each episode focusing on a species, and each season focusing on a theme. Season 1 is about dynasties, and episode one focuses on Carcharodon megalodon. I’m excited about this podcast; Sean has a dynamite radio voice and stylistically it’s sort of a paleontology-version of This American Life. Rather than fanboy gushing over mega-sharks, he tells the story of the role C. megalodon played in understanding what fossils are, and how they shaped our understanding of past life being different. Dragon Tongues is kid-appropriate and non-scientist accessible.

For more Dragon Tongues,  follow it on Twitter and subscribe on iTunes.


If your main source for podcasts is iTunes, that’s it. Those are the only four paleo-only podcasts they host. However, there are several other science-themed podcasts aimed for a general audience, that feature paleontological topics.

Tetrapod Zoology is a relatively new podcast hosted by SciAm blogger Darren Naish and palaeoartist John Conway. As with the blog, its topics include vertebrate paleontology in addition to the biology of living tetrapods, science fiction movies, and cryptozoology. These topics are all mixed into each ~60-90 minute episode, so there are no pure-paleo shows (so far). Recent episodes include discussions of woolly rhinos, mesosaurs (fossil vertebrates somewhat closely related to reptiles), and the tail of Jeholornis (a fossil bird from the Cretaceous of China). The show jumps right into the topic, and usually begins with zoology or paleontology. It shares the tone that makes the original blog work so well; Darren and John are both genuinely interested and it shows. It would be cool if they added links to the papers/books being plugged/discussed to the website, but it’s still new, so maybe this will happen in the future. The shows are kid-friendly and generally accessible to non-scientists (they explain technical stuff), but as I said above, not paleo-exclusive.

Follow TetZoo on their website and subscribe on iTunes. Also, you really should read the blog itself.

radiolab logo

Nothing else sounds like Radiolab. You might have heard it on public radio; it’s nationally syndicated. Each week, a different topic (often scientific, sometimes news or philosophical) is explored, presented from the perspective of the hosts as if they are learning about it in real time. Clips from interviews are woven into the discussion, so listeners follow how the scientists made their discoveries and changed their thought processes. Check out this recent ep in which University of Chicago paleontologists discuss using fossil corals to track changes in the number of days per year through time. Definitely kid- and non-scientist friendly: anyone who is natively curious about the world should like it. It’s one of my favorites, even when the topic isn’t science.

Follow Radiolab on their website, Twitter, Facebook, or iTunes.

science friday

Science fans are probably already familiar with the weekly Science Friday podcast, which is also aired on public radio stations across the US. Each week, host Ira Flatow examines several topics from recently published research, including short interviews with the researchers themselves. Recent episodes include discussions with NSCU grad student Edwin Cadena about car-sized giant turtles from Colombia and a conversation about Utah’s fossil history with Utah professor Dr. Randy Irmis, science writer Brian Switek, and BYU professor Dr. Brooks Britt. And just last week, Dr. Ted Daeschler from the Academy of Natural Sciences, Philadelphia was on the show to chat about the hind limbs of Tiktaalik. Go! Subscribe! Now!


Given that people find paleontology so fascinating, it’s really weird that there aren’t more dedicated paleo-podcasts. I would have assumed  that there would at least be one weekly or bi-weekly “dinosaur roundup” show…

Do you blast your quads to a different science podcast? Have I missed some in this list? Let me know in the comments section!

Category: Miscellaneous, Paleontology | Tagged , , | 5 Comments

Sharing Phylogenetic Data — Public Comment Invited

Data sharing is important–it helps scientists to reproduce others’ results, add data to previous analyses, and otherwise maximize the impact of an individual publication. This isn’t really news, of course. But, now that we are in a world where data sharing is increasingly the norm, how do we make sharing as easy as possible? It’s not enough to slap some tables up on a personal website or even on an official data repository; the data have to be easily readable by humans and machines, easily reusable, and easily accessible for the long term.

One major goal of biology is to understand the arrangement of the branches on the Tree of Life (phylogenetics). Beyond the general drive to understand what is most closely related to what, a solid tree can help answer all sorts of interesting questions about the patterns and process of evolution. How did gigantism evolve in some dinosaurs? How did bird brains evolve? How did bone-cracking dogs get their beefy skulls? Of course, published trees are “just” hypotheses. The arrangement changes slightly (or occasionally even radically) with the discovery of new species, sequencing of new genomes, development of new tree reconstruction methods, and reinterpretation of old anatomy. Thus, data sharing is crucial for phylogenetics–scientists need to be able to add data, reanalyze old data sets, and reevaluate previous work in order to have the best possible tree.

Evolutionary trees help scientists understand the evolution of bird brains. Image from Smith and Clarke 2012. CC-BY.

Evolutionary trees help scientists understand the evolution of bird brains in concert with the evolution of their lifestyles. Image from Smith and Clarke 2012. CC-BY.

Data tables form the core of phylogenetic analyses, whether the data are in the ACGT of a DNA sequence or the 1′s and 0′s that mark presence or absence for the anatomy of a fossil organism. Alongside the data table are lists of characters, lists of specimens, and all of the other important supporting information. This makes for a complex situation, and there is considerable variability in how different researchers, and even different publishers, present these critical data. Standardization is a must!

Karen Cranston, Luke Harmon and Maureen O’Leary, lead researchers on the NSF-funded “Assembling, Visualizing, and Analyzing the Tree of Life” (AVAToL) project, are drafting a document that lays out best practices for sharing phylogenetic data. This includes trees, aligned gene sequences, data matrices, character lists, and all of the other technical details that underpin an analysis. Maureen relayed to me that she is particularly interested in comments on how to deal with time and other metadata. Are you someone who works with or is interested in phylogenetic data? They’re looking for your input!

The draft “best practices” guidelines are available as a Google Document, freely editable by anyone. In particular, input is requested on guidelines for data storage and formatting. The coordinators for this effort request your comments soonJanuary 22 or 23 at the latest, so act now if you are interested! There are already some great comments on the document.

I applaud the steps that Cranston, Harmon, and O’Leary are taking to make this a true community effort. Too often these kinds of “best practices” documents are crafted in the proverbial “smoke-filled back room,” catering to a handful of insiders. The more open the process, the better the guidelines and the more likely people are to use them! May this serve as a model for future efforts.

Want to add your input? Check out the draft guidelines for more information! 

Category: Miscellaneous, Open Data, Paleontology, Zoology | Tagged , , , , , | 2 Comments

Ichthyosaur is the New Black

Just yesterday, a group of 2nd graders asked me what color dinosaurs were. I was pretty excited to tell them we actually do know this through looking at tiny structure on feathers called melanosomes. Melanosomes are sub-millimeter sized round or cigar shaped organelles inside of animal cells that contain melanin, the substance that causes pigmentation. When we examine melanosomes in modern organisms, their chemical profiles (known as a spectra) tells us what type of melanin is in that melanosome. Eumelanin is responsible for black and brown pigment and pheomelanin is responsible for red or pink coloration. Carotenoids and porphyrins are other non-melanin pigments, and can produce other colors in birds like bright yellow and green. Interestingly, a blue coloration is produced not by pigment but the scattering of light from unique keratin ‘air pockets’ in certain type of bird feathers. This means blue is a structural, not a pigmented color.

Different types of melanin are really the easiest for us to distinguish in fossil specimens due to the fact their chemical profiles are preserved in melanosomes. From this type of research on dinosaurs, we have found out that Microraptor was shiny and black. A feather from the 1861 Archaeopteryx specimen indicates it too was black. This research, up until this point, has mostly focused on examining the melanosomes in birds, but this week, in Nature, this same idea was used to determine the colors of ancient marine reptiles.

This time, Johan Lindgren and coauthors were interested in the colors of extinct marine giants like ichthyosaurs, the mosasaur Tylosaurus, and an extinct leatherback turtle. Scrapings of “skin” were taken from these specimens and put into some special microscopes. The skin of these specimens is a blackish sort of film that, to the naked eye, doesn’t look like anything special. But up close in the scanning electron microscope, it is immediately apparent that the telltale cigar-shaped melanosomes are present. It is important to note fossil bacteria can look very similar to fossilized melanosomes, but distinct chemical signatures only on the body areas of the fossils and not on the sediment outside that zone seem to indicate they were present in life and did not form after death.

The chemical profiles of the melanosomes in all three of these marine reptiles indicated they were black in color because eumelanin was detected. Interestingly, it seems the ichthyosaur was black on the entire body- not just on the dorsal side. The mosasaur and turtle possibly had a dark top and a lighter underside. You may be wondering why any of this matters- what difference does it make if an ichthyosaur was black all over? In the paper, the authors aptly mention coloration is a trait that is subject to natural selection. Coloration in animals influences sexual displays, thermoregulation, and camouflage.  Certain animals can be better adapted to colder environments if their dorsal sides are darker in color, which will allow them to absorb more heat. Cordylid lizards in South Africa that had lower skin reflectance (more melanin) had a higher fitness than species that had lighter, more reflective skin.

Ichthyosaur specimen from the Alf Museum. Courtesy of Andy Farke. CC-BY

Ichthyosaur specimen from the Alf Museum. Courtesy of Andy Farke. CC-BY

Ichthyosaurs may have had eumelanin on their entire body due to a benefit in thermoregulation. If they spent time close to the surface, they could absorb more sunlight and stay warmer in cold environments. Extant leatherback turtles are dark on the top of their shells, possibly for this reason. This pigmentation pattern is called thermal melanism. On the other hand, most turtles and cetaceans are countershaded–dark on top and light on the bottom. This shading in cetaceans seems to obscure their own shadows while they are diving, making it easier to sneak up on prey. Species of whales that possess uniform dark coloration could be better adapted for diving to extreme depths where there is no light, but the evidence for this is mostly anecdotal at this time.

This study indicates for the first time there is convergent evolution of melanism in secondarily aquatic tetrapods, but more importantly expands fossil melanosome analysis beyond just feathers. Not that long ago, determining the color of extinct animals seemed impossible, but now it is very clearly possible for more organisms than we ever imagined!


Carney, R. et al. 2012. New evidence on the colour and nature of the isolated Archaeopteryx feather. Nature Communications. 3 (637). doi:10.1038/ncomms1642

Clusella-Trullas, S., Hvan Wyk, J., Spotila, J.R. 2009. Thermal benefits of melanism in cordylid lizards: a theoretical and field test. Ecology 90:2297–2312.

Li et al. 2012. Reconstruction of Microraptor and the Evolution of Iridescent Plumage. Science 335 (6073) 1215-1219. DOI: 10.1126/science.1213780

Lindgren, J. et al. 2014. Skin pigmentation provides evidence of convergent melanism in extinct marine reptiles. Nature. doi:10.1038/nature12899

Category: Dinosaurs, Geology, Paleontology | Tagged , , , , | 3 Comments

Q&A with Daniel Field–Weighing Dead Birds

Although we can directly weigh modern birds, we can’t do this with extinct birds–and we need to know body mass to understand their biology! The previous post on this blog reviewed a newly published PLoS ONE paper on how to accurately estimate the mass of a bird from measurements of its skeleton. The senior author on that paper, Daniel Field, was kind enough to answer a few questions about the research and tell us some anecdotes that didn’t make it into the formal publication.

Daniel Field, lead author of the recent study on body mass estimation in birds, with a red-winged blackbird that escaped inclusion in the sample. Photo courtesy Daniel J. Field.

Daniel Field, lead author of the recent study on body mass estimation in birds, with a red-winged blackbird that escaped inclusion in the sample. Photo courtesy Daniel J. Field.

What was the inspiration for your research? 

As you mention in the introduction to your [previous] blog post, body mass correlates with many important biological parameters. Therefore, having an idea of how much a fossil organism weighed can provide important clues about its lifestyle–clues that may otherwise be difficult to infer. Although a considerable body of work presenting methods for estimating the body mass of fossil birds already existed, I was troubled by the fact that most studies investigating fossil body mass only quantify a single, mean mass estimate. This approach is problematic, since a considerable amount of uncertainty exists in our attempts to estimate fossil body mass; only presenting a single, mean estimate oversimplifies the situation, and runs the risk of making estimates seem speciously precise. With our study, we attempted to address this issue by providing simple methods for estimating well-justified 95% prediction intervals for fossil mass estimates.

Was this paper part of a larger project, or an isolated study?

This work constitutes a portion of my PhD dissertation, which will seek to apply well-justified body mass estimates to a variety of interesting problems in bird evolution.

You spent a lot of time in the Yale Peabody Museum collection gathering data for the study…is there any specimen from the project that sticks out in your mind as particularly interesting?

One thing that really emerges when you spend time looking at bird skeletons is the incredible disparity in their hindlimb proportions. Unlike in humans, where the femur and tibia constitute the vertical portion of the leg, the vertical portion of a bird’s leg is composed of the foot (the ‘tarsometatarsus’) and the tibia (‘tibiotarsus’ to be precise). Some of my favourite birds are waders and shorebirds (like herons, flamingoes and sandpipers), which exhibit some of the most extremely elongated hindlimbs in nature. I find the supremely elongated tarsometatarsus of stilts (aptly-named shorebirds of the genus Himantopus) to be some of the most graceful bones in any museum collection. Here’s a link to an image of a flying stilt in Spain, showing off its gangly legs.

Black-necked stilt (Himantopus mexicanus), showing off its amazingly gracile and elongated legs. Image by flickr user winnu - CC-BY 2.0.

A black-necked stilt (Himantopus mexicanus), showing off its amazingly gracile and elongated legs. If you’re not familiar with bird anatomy, you will probably be surprised to learn that the part below the bend in the leg on the animal in this picture (including the tarsometatarsus bone)–is equivalent to most of the sole of our foot. Image by flickr user winnu – CC-BY 2.0.

What was the most challenging part of this project?

With a project of this scale, a challenging issue that emerges is simply one of data management; with approximately 12,000 spreadsheet cells of raw data, simple frame-shift errors can have huge consequences! This was something that we all needed to be mindful of when inputting data, performing analyses, and making corrections.

You used the open source statistical software R for data analysis…how was that experience for you and your co-authors? Did you have much background with the software before this project?

At the outset of the study, only one of our group members (Simon Darroch) had much experience working with R, so his analytical work was crucial. At the time, the prospect of analyzing this much data seemed really daunting to me. However, I had the chance to participate in a statistical workshop geared towards palaeontologists last summer, which gave me my first exposure to R and taught me many skills that will be useful moving forward. Most of the analyses that we present are actually really simple to implement in R, as long as you have a bit of a background.

Thank you, Daniel, for telling us the story behind the paper! If you want to learn more, you can check out his personal website, read my blog post about the body mass estimation paper, or read the paper itself at PLoS ONE.

Field DJ, Lynner C, Brown C, Darroch SAF (2013) Skeletal correlates for body mass estimation in modern and fossil flying birds. PLoS ONE 8(11): e82000.doi:10.1371/journal.pone.0082000

Category: Interview, Open Access, Paleontology, PLOS ONE, Zoology | Comments Off