Behind the Scenes at PhyloPic

Open science is about more than just tossing some publications and data notebooks into the digital ether. It’s all about communication–so, at this point I’m obligated to say that “A picture is worth a thousand words.” One of my favorite open-friendly image sources is PhyloPic, a phenomenal site with over 2,200 silhouettes of organisms past and present. These silhouettes can be quite handy to illustrate family trees (for instance, we used them in our paper on the horned dinosaur Aquilops), or blog posts, or public presentations. Suffice to say, it’s a great resource. [full disclosure: I have contributed some images to the site]

To learn more about PhyloPic, I invited founder Mike Keesey to share his perspective.

A gull, Larus. Public domain image by Mattia Menchetti, via PhyloPic.

A gull, Larus. Public domain image by Mattia Menchetti, via PhyloPic.

Can you tell us a little bit about the genesis of PhyloPic? Where did the idea come from?
Well, Andy, as you remember, back in the late ’90s and early ’00s, I used to run a website called The Dinosauricon, which featured dinosaur information and illustration [note from Andy: you can view the version from 2000 on the Wayback Machine at Internet archive]. There were pages for every genus in the avian stem group (not just dinosaurs). And there were thousands of illustrations from dozens of contributors. I was never satisfied with it, though. I had these increasingly grandiose plans to do a complete redesign. But, after several aborted attempts, I had to face the fact that I would never, ever have enough time to complete it. In fact, by that point I didn’t even have time to maintain the site as it was. I eventually let it die.

As the years went by, I’d occasionally look into the idea of reviving it, but it seemed like other websites were doing a better job at its core missions. Wikipedia is an amazing resource for up-to-date dinosaur information, far better than the Dinosauricon ever was. And for illustrations we have image search services, Wikimedia Commons, DeviantArt, Flickr, and so on.

So I tried to think of something the Dinosauricon had done that wasn’t being done better by something else. And I recalled the silhouettes. Every taxon page had a representational silhouette, made by myself or Frank DeNota. But instead of making hundreds of silhouettes, I just reused several dozen, since related dinosaurs mostly have similar silhouettes. (Except for those dang ceratopsids!) In doing this I had been inspired by a product from my childhood: Safari Cards. For those who’ve never heard of them, they were a series of collectible cards about animals, including a taxonomic organization system that used silhouettes as a visual key. Another inspiration was David Lambert’s A Field Guide to Dinosaurs, one of my favorite books from childhood.

A lot of people had reused Dinosauricon silhouettes in diagrams for presentations and classroom material. Silhouettes are a really common need for researchers and educators. So I thought, what if I were to chuck all those grandiose plans, and narrow the scope? A website with freely reusable silhouettes. That’s it. Nothing else. And, like the Dinosauricon, I wanted to make it possible to use the same silhouette for related taxa. By using a third-party resource for the taxonomy (uBio), I could even expand the taxonomic scope without too much extra effort — not just dinosaurs, but all life forms. Finally, I had a project I was able to complete!

Giraffatitan, CC-BY, by Matt Wedel via PhyloPic.

Giraffatitan, CC-BY, by Matt Wedel via PhyloPic.

What has been your favorite use of imagery from PhyloPic?
I think I’m still waiting for it. I mean, I’m ecstatic that a lot of researchers and educators are using PhyloPic silhouettes in their diagrams, and that developers have built tools that use the API. (If you use R, check out Scott Chamberlain’s rphylopic package. The Open Tree of Life also uses the API to grab silhouettes for its pages.) These are exactly the sorts of usage I had hoped for from the start.

But I haven’t seen designers or animators really latch onto it yet, except as silhouette contributors. I think there are opportunities to create amazing pieces using PhyloPic silhouettes, but I’m still waiting for someone to blow my mind with something I never thought of. In the meantime, though, I’m just glad that more and more people are finding it useful.

You use a mix of licenses (Creative Commons, Public Domain, etc.) on the site. How, in your view, has this played out in the “real world”?
I had to make some tough choices early on. Creative Commons has several different licenses with various restrictions. Initially I just wanted to provide three choices: public domain, attribution, and attribute/share-alike. But some artists I talked to also wanted a noncommercial option. I seriously dislike the Creative Commons NonCommercial component, because it’s worded so broadly that it disallows almost any online usage. Wikipedia and Wikimedia can’t use noncommercial works, for example, even though they’re nonprofit organizations. But I really wanted to build up as large a bank of images as possible, so I grudgingly relented. (And note that you can usually contact the artist if you need them to waive that component of the license for you.)

As for how it has all played out — well, it’s funny that the entire point of Creative Commons is to simplify licensing for free reuse, and yet many people still don’t follow the terms! Maybe their eyes just glaze over when looking at the bullet points, I don’t know. But I see it all the time. People use a silhouette that’s under an attribution license, but don’t credit the artist. (Often they credit “PhyloPic”. While I always appreciate the site being mentioned, it is not itself an artist.) Or people use a silhouette that’s under a noncommercial license in a subscription-based journal, or they use a silhouette that’s under a share-alike license in a diagram that is not itself under a share-alike license. Quite often the license isn’t mentioned at all.

I think part of the problem is that silhouettes aren’t seen as “real” artwork. People see “freely reusable” and just think they can grab them with no further obligations. Now, granted, some of them didn’t require much effort to make, such as the ovoid I use to represent cellular life — although that one’s public domain! But many others are the result of hours of tedious work. On behalf of the artists, I’d like to exhort people using the silhouettes to take a closer look at the license terms. The creators are not asking for money, just some consideration. Please respect the work that went into creating the art. (Unless they’re public domain — then do whatever you want.)

I do want to make this easier for users. I’ve recently moved the license bullet points to a more visible spot on the image pages. And one of my highest priorities is to enable users to manage collections of silhouettes. Collections will include automatic attribution generation and license selection. I think that will be hugely helpful.

And if anyone else has ideas to make this easier, let me know! From anywhere on the site, just click“Dev > Request Feature”.

The gerenuk, Litocranius walleri. CC-BY, by Andy Farke, via PhyloPic.

The gerenuk, Litocranius walleri. CC-BY, by Andy Farke, via PhyloPic.

Do you have any long-term dream for PhyloPic? Where do you see the site in two years? Five years?
For me, the beauty of PhyloPic is that it’s useful the way it is right now, but you could still spend a lifetime fleshing it out. I can very easily see myself as an old man still finding neglected groups, fixing up their taxonomy, and adding illustrations. The Tree of Life is just so vast.

I have a lot of technical improvements and new features I want to add, too. You can see them on the site, under “Dev > Road Map”. One big one will be automated cladogram generation. The idea is that you plug in a Newick string and it spits out an illustrated, linkable cladogram — that would be incredibly useful. And I could even capture phylogenetic information from that and feed it back into the taxonomy!

Eventually I want to add other types of images, too, not just silhouettes. Imagine being able to do a taxonomic search for photographs, restorations, skeletal reconstructions, whatever. But I don’t want to take that on until I’ve “mastered” silhouettes. And I think I have a long way to go.

The scope of PhyloPic is pretty ambitious. What areas would you like to see with more imagery?
Oh man, where to begin? There’s a huge emphasis on “charismatic megafauna” right now. While we are starting to get better coverage for some other groups (for example, Birgit Lang’s contributions for soil organisms), there’s a long way to go. And even most groups of charismatic megafauna aren’t that well covered. As of right now there are only 2,264 silhouettes on the site, covering millions and millions of species.

I guess if I had to make one suggestion for people who want to contribute but aren’t sure what they want to do: plants. Please, we need more plants.

Thanks, Mike! For those of you readers who haven’t yet checked out the PhyloPic website, I encourage you to do so.

Portura by Birgit Lang. CC-BY, via PhyloPic.org.

Protura. CC-BY, by Birgit Lang, via PhyloPic.org.

Category: Art, Open Access, Open Data, Paleontology, Technology | Tagged , , , | Leave a comment

Welcome, Wendiceratops!

It’s a very exciting time to be a paleontologist interested in horned dinosaurs. New species are being described at an incredible rate. But, it’s not the fact that they are new that’s important–it’s what the fossils say about the evolution, anatomy, and lifestyle of Triceratops and kin. Wendiceratops is the latest in this paleontological parade.

Wendiceratops in life, as restored by artist Danielle Dufault. CC-BY, from Evans and Ryan 2015.

Wendiceratops in life, as restored by Danielle Dufault. CC-BY, from Evans and Ryan 2015.

Wendiceratops roamed southern Alberta around 79 million years ago, when the area was a lush lowland on the western edge of a seaway covering the middle of North America. Parts of at least four Wendiceratops were found together, including a mix of younger and older animals. None are complete, but enough is preserved to allow a fairly detailed reconstruction of the overall anatomy.  Wendiceratops is unique among horned dinosaurs in the configuration of the forward-hooked bones studding the back of the frill. Each species has its own “fingerprint” of frill bones, so it’s pretty easy to pick out Wendiceratops from the crowd of its close relatives.

To me, it’s quite interesting that the frill of Wendiceratops is similar (but not identical) to an animal called Sinoceratops, which lived a few million years later in China. This suggests a close evolutionary relationship between the two animals. Does it mean that Wendiceratops or one of its descendents wandered over to China from North America? That’s certainly possible, and warrants additional study. Horned dinosaur skulls are developmentally plastic, so it’s also possible that the anatomy in Sinoceratops was independently evolved. We’ll need more fossils to figure this out!

Skeleton of Wendiceratops

Skeletal reconstruction of Wendiceratops, with known bones shown in blue. CC-BY, by Danielle Dufault, from Evans and Ryan 2015.

Like many of its close relatives, Wendiceratops had a big nose horn. This in itself is not unusual, but within geological time Wendiceratops is the oldest horned dinosaur to have the feature. Paleontologists have suspected for awhile that enlarged nose horns evolved at least twice in horned dinosaurs (once in the line leading to Triceratops and once in the line leading to Wendiceratops and its relatives…and maybe a third time in the “primitive” Protoceratops). Now we know a little more about the timing! Fossils like Wendiceratops add critical details to the broad-brush evolutionary picture.

Wendiceratops (named in honor of its discoverer, Wendy Sloboda) was announced today by David Evans and Michael Ryan, in a paper appearing in PLOS ONE. The authors promise another manuscript focused on the back end of the animal (the postcrania), so we can look forward to more Wendiceratops in the near future!

Citation
Evans DC, Ryan MJ (2015) Cranial anatomy of Wendiceratops pinhornensis gen. et sp. nov., a centrosaurine ceratopsid (Dinosauria: Ornithischia) from the Oldman Formation (Campanian), Alberta, Canada, and the evolution of ceratopsid nasal ornamentation. PLoS ONE 10(7): e0130007. doi:10.1371/journal.pone.0130007

Category: Dinosaurs, Paleontology, PLOS ONE | Tagged , , , , , , , | 1 Comment

Fossil Lizard Showcases Wyoming’s Tropical Wonderland

Wyoming is a beautiful place, but usually it is associated more with open range, cowboys, mountains, and skiing than it is with palm trees and alligators. What a difference 48 million years makes!

Fossils in the rocks of the Bridger Formation, spanning part of the Eocene epoch from around 49.5 to 46 million years ago, reveal a Wyoming covered by tropical forests and filled with alligators, early primates, and giant lumpy-headed herbivores. To top it off, average temperatures were probably around 9°C (16°F) warmer than today. These conditions present a tidy historical experiment to see how life responds to elevated temperatures, both in terms of evolutionary change as well as geographical distribution.

Fossil skull

Fossil skull of Babibasiliscus, modified from Conrad 2015. The nose is to the right of the image. CC-BY.

As temperatures warm in temperate zones, it is not unusual for otherwise equatorial organisms to make their home in formerly chilly climes. Thus, the newly named fossil lizard Babibasiliscus alxi is yet another example of Wyoming’s tropical connections. Babibasiliscus, which lived around 48 million years ago, is most closely related to today’s casquehead lizards. Perhaps the best known contemporary example is the basilisk lizard, also called the “Jesus Lizard” for its ability to run across the surface of standing water for short distances.  The nine modern species of casquehead lizards are exclusive to the New World, ranging from Ecuador up to Mexico.

Babibasiliscus was described this week in PLOS ONE, by lizard paleontologist Jack Conrad. An analysis of the evolutionary relationships of lizards show that Babibasilicus and another extinct lizard (Geiseltaliellus, which lived around the same time in Europe) are comfortably nested well within the evolutionary branches of casquehead lizards. Not distant cousins, not some long-lost ancestor–real, genuine, bona fide casquehead lizards! This strongly suggests that the exclusively neotropical distribution of today’s lizards is an accident of history. Perhaps they even originated outside of the equatorial zone–contrary to hypotheses based solely on analysis of genetic data from modern lizards. A proud lizard empire that once spanned continents has been defeated…well, perhaps that is a bit of an exaggeration, but you get the idea.

Babibasiliscus is a wonderful example of fossils showing up in unexpected places. As the world has changed, the distributions of its animals and plants change too. The fossil record is the best tool to show this!

Laemanctus longipes, one of the closest living relatives of Babibasiliscus. Image by Vassil, CC0.

Laemanctus longipes, one of the closest living relatives of Babibasiliscus. Image by Vassil, CC0.

Citation
Conrad JL (2015) A new Eocene casquehead lizard (Reptilia, Corytophanidae) from North America. PLoS ONE 10(7): e0127900. doi:10.1371/journal.pone.0127900

Category: Climate Change, Paleontology, PLOS ONE, Zoology | Tagged , , , | 1 Comment

Guest blog: A Missed Opportunity for Paleontologists

[From time to time on The Integrative Paleontologists, we will invite guest bloggers to share alternate viewpoints about current topics. Today’s guest post is by Matthew Brown, who previously posted about the impact of new regulations on fossil collection from federal lands.]

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Ask any paleontologist how they chose their field, and one of the most frequent responses that you would hear is “I always loved dinosaurs as a kid, and just never grew out of it.” Like astronaut or firefighter, the job of paleontologist is certainly a title that many children aspire to hold, and we often refer to paleontology as a “gateway drug into science.” Dinosaurs have captured the public imagination since their discovery, and for nearly 200 years have starred in books, cartoons, and movies. They have advertised gas stations and inspired as the centerpiece of blockbuster museum exhibits. This weekend, the film Jurassic World broke domestic and international records, grossing $524.1 million worldwide, and once again will expose a generation to the excitement of watching genetically re-engineered extinct animals running amok. And paleontologists aren’t happy about it.

In 1993, the film Jurassic Park revolutionized the way the public looked at dinosaurs, and helped to draw attention to the paradigm shift that took place in the way we study and interpret past life. New books and courses in paleontology flourished, and more than a few working scientists today can trace their introduction to the science through the Jurassic Park novels and movies. In recent months, however, the professional paleontological community has leveled numerous criticisms against the scientific accuracy of the new installment in the franchise.  Through articles and opinion pieces in National Geographic, The Guardian, Scientific American, The Telegraph, CBS, CNN, and the New York Times, scientists have roundly attacked the Jurassic World filmmakers for failing to make the new villains of their monster movie look like our current interpretations of dinosaurs and other prehistoric reptiles. Despite one character in the movie itself reminding us “nothing in Jurassic World is natural,” real-life scientists are admonishing Hollywood for a failure to educate. Some have voiced concerns about the “dumb questions” that they might field from a confused public. While nitpicking a lack of animated feathers or implausible communication between raptors, critics have yet to provide a compelling explanation for why getting the facts right matters. So why study paleontology, or any other natural science? This is the big picture question lost in the pedantic static, and I believe it to be the real missed opportunity.

We certainly know more about dinosaurian biology today than we did 22 years ago. But at the same time, according to surveys by the National Science Foundation, only 48% of the American public accepts human evolution. There is scientific, but not political, consensus on climate change. Congress has proposed massive cuts to the Earth Sciences budgets of the National Science Foundation and NASA, and last week the governor of Illinois proposed shutting down the Illinois State Museum.  Far from the dusty storehouses as they are commonly portrayed, museums, along with universities, are this nation’s factories for knowledge generation. This new knowledge will be key to humanity’s food, energy, and water security, to continued advances in medicine, space exploration, extinctions, and understanding of our climate. A country who doesn’t understand how that knowledge is generated and used will probably be reluctant to fund it. Science requires a childlike curiosity and openness to accept new information, for permission to be wrong. But it just as much needs us to be grownups, to explain (and recognize) the consequences of action and inaction.

 

See real dinosaurs at the McClung Museum

The McClung Museum gets it! They tied in the JW opening with museum discounts. Image © 2015 Stephanie Drumheller and used with permission.

Few people enter the natural sciences for high pay or glamour. Instead, we are compelled to answer questions about the world and universe around us, to gain new insights into the story of our planet and its life. This is the opportunity for paleontologists to be those ambassadors for science, using the international stage that a movie like Jurassic World provides to get people excited. It should be no surprise that scientists with advanced degrees in a field know more than producers, directors, writers, and other members of the general public; but instead of fact checking them at every turn, let’s walk that public through the same joy of discovery that we experience every day. In the film, a child runs past a theme park display on genetics shouting something like “ACTG! The building blocks of life!” How often do you hear that in a museum? In my 20-year career, not once. Paleontology is on the cultural radar, and we paleontologists should be relishing the opportunity to engage, and remembering that there are no dumb questions, especially when they come from children. Rather than behaving like, well, boneheads.

Matthew A. Brown is Director of Museum Operations at the Vertebrate Paleontology Laboratory and Lecturer in the Department of Geological Sciences, The University of Texas at Austin.

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NB from SW: I want to commend one museum, the McClung Museum of Natural History and Culture at the University of Tennessee in Knoxville, whose pic is shown above. They had a great tie-in with the Jurassic World opening, including movie posters advertising museum discounts to moviegoers, fossils and dino species info on display at the theater, and a dino-themed summer camp. You can check out pics and get more info on their Facebook page or Twitter. Some scientists and museums did get it right – by using the movie as an opportunity to capitalize on interest, they educated the public in a positive way (i.e., doing more than nitpicking). Great job, McClung Museum! And thanks to Dr. Stephanie Drumheller for tipping me off on their great efforts!

Category: Dinosaurs, Miscellaneous, Navel Gazing, Paleontology | Tagged , , | 3 Comments

The Curse of the Horned Dinosaur Egg

Horned dinosaurs (ceratopsians) just can’t catch a break when it comes to their fossilized eggs. The first purported examples turned up in Mongolia during the 1920s, attributed to Protoceratops. A few unlucky “Protoceratops” eggs were fossilized next to the jaws of another dinosaur (Oviraptor, which means “egg thief”), presumably in the act of raiding the nest. Decades later, it turned out that the nest raider was probably the parent Oviraptor safeguarding its own eggs. Study of other eggs associated with embryos showed that everything we thought were Protoceratops eggs were actually from Oviraptor and related animals!

A nest of Oviraptor (formerly Protoceratops) eggs on display at the American Museum of Natural History. Image by Steve Starer, CC-BY.

A nest of Oviraptor (formerly Protoceratops) eggs on display at the American Museum of Natural History. Image by Steve Starer, CC-BY.

So, as a horned dinosaur fancier, I was pretty excited when an authentic ceratopsian egg and embryo were announced in 2008. Amy Balanoff and colleagues described an egg from Late Cretaceous-aged rocks (~90 to 70 million years old; the exact date is uncertain), which had a few tiny bones poking out of the end. Dinosaur embryo! Computed tomography (CT, a technique using x-rays to peek inside objects) revealed more of the bones, including two skull bones that appeared especially ceratopsian. One bone was identified as a predentary, the scoop-shaped bone at the front of the lower jaw used to lop off plants. The other skull bone appeared to be a quadrate, one of the bones of jaw joint. The predentary in particular narrowed identification to a plant-eating dinosaur (the bone doesn’t occur in theropods such as Oviraptor), and the shape of the quadrate further suggested a horned dinosaur. Yamaceratops (closely related to Protoceratops) is a ceratopsian found in the same rock layers and was thought to be the likely source.

One puzzle, though, was the eggshell itself. Eggshell appears simple to the naked eye, but the microscopic details can be pretty distinctive to the egg producer. The number of layers within the eggshell, for instance, and the arrangements of the minerals that make up the layers, vary from group to group. Some eggshells, such as those of turtles, have but a single layer. The Mongolian ceratopsian eggshell had three layers–a characteristic usually associated with theropod dinosaurs (Oviraptor and early birds, for instance). But, given the presence of ceratopsian bones in the egg and the fact that nobody knew what ceratopsian eggshell should look like, this suggested that horned dinosaurs had eggshell that converged on that of theropods. So, the three-layered eggshell evolved multiple times across dinosaurs.

"Protoceratops BW" by Nobu Tamura (http://spinops.blogspot.com) - Own work. Licensed under CC BY 2.5 via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Protoceratops_BW.jpg#/media/File:Protoceratops_BW.jpg

Protoceratops, by Nobu Tamura. CC-BY 2.5.

But…things are never that simple. A new paper in PLOS ONE, including the two senior authors from the original work, proposes a new identification. Ceratopsian no more…now it’s a bird!

Incredulity might be the first reaction of many people. How could you mix up a wingy, feathered bipedal thing with a big plant-munching quadruped? It should be obvious to even a casual observer, right?

Actually, no. Embryonic bones (those inside of an egg) can look vastly different from those of their adult counterparts, because many characteristic features don’t appear until the animal is out of the egg. As a result, it can be tough to orient and identify bones correctly. Additionally, even high-tech imaging (such as CT scanning) has a certain degree of interpretation to it. The researcher who digitally separates bone from rock has to make judgement calls all of the time. Is this bone or rock that looks like bone? Are these two bones stuck together, or one bone with a crack down the middle? Even under the best of circumstances, there is room for ambiguity.

Given what everyone knew at the time, and in light of the possible predentary and other bones, “ceratopsian” was a reasonable hypothesis as presented in the initial publication. But a second look at the data never hurts. Movies of the CT scans were posted online, allowing other researchers to take a peek. Undoubtedly following some pretty interesting discussions, two of the original authors (Amy Balanoff and Mark Norell) joined dino-bird expert Dave Varricchio (lead author on the new paper) to present a re-interpretation of all of the data.

Bird bones, with silhouette of an enantiornithine.

Bird bone pick-up sticks! At left, the digitally isolated bones from within the Mongolian bird egg. At lower right, the left hind limb bones within the egg (ghosted outline). In the original paper, the femur (yellow) was interpreted as a humerus. The silhouette in the upper right shows the appearance of a closely related Cretaceous bird, Protopteryx (image by Matt Martyniuk via PhyloPic.org, CC-BY). Fossil imagery modified from Varricchio et al. 2015. Scale bars equal 5 mm (left) and 10 mm (right).

It turns out that the egg was turned around in the original interpretation; the front of the animal could be identified instead as the back. Thus, many of the bones were mis-oriented in the original paper. What was thought to be a ceratopsian humerus turned out to be a bird femur, a tibia turned into an ulna, and so on. As described above, this is a pretty easy “mistake” to make, given how nondescript many embryonic bones are. The quadrate and predentary are more mysterious–the former may be a pelvic bone, but the true identification of the “predentary” is highly debatable. Perhaps it’s part of a vertebra, or a wishbone, or something else. In any case, when reoriented, most of the bones are a better match for bird than ceratopsian.

If the Gobi egg is from a bird, that also solves solves the problem of the three-layered eggshell. No longer distributed across dinosaurs, this type of eggshell is now firmly restricted to theropods (including many birds). Additionally, this embyro provides another rare data point for studying the embryology of ancient birds. Previous discoveries have shown some key developmental differences between non-avian dinosaurs, early birds, and modern birds, so the newly identified Gobi bird egg has an important story to tell on how these differences evolved over time.

One mystery remains–what do horned dinosaur eggs and embryos look like? There are undoubtedly unidentified examples in a museum drawer or outcrop. A nest of little Triceratops sure would help right about now.

Citation
Varricchio DJ, Balanoff AM, Norell MA (2015) Reidentification of avian embryonic remains from the Cretaceous of Mongolia. PLoS ONE 10(6): e0128458. doi:10.1371/journal.pone.0128458

Paleontology confession: I was an anonymous reviewer for the 2008 paper, and the predentary identification in particular was compelling support for calling it ceratopsian. Based on what the authors presented in 2008, and based upon the figures and interpretations available at the time, I thought there was a slim possibility the egg could be another kind of plant-eating dinosaur, but the thought of “bird” never crossed my mind. Seeing the new paper, “bird” is pretty blindingly obvious in the end, but that is only with the benefit of 20/20 hindsight, re-orientation of the specimen, and a whole bunch of additional information. I suppose this case is a good anecdata point showing how peer reviewers can be wrong sometimes.

Category: Birds, Digitization, Dinosaurs, Paleontology, PLOS ONE, Technology, Zoology | Tagged , , , , , , , , , , , , | 4 Comments

Guest Post: Can We Easily Distinguish Male and Female Protoceratops?

This guest post is from Leonardo Maiorino, a vertebrate paleontologist with a particular interest in understanding the evolution of the skull in horned dinosaurs. Leo was at the helm of a recent paper in PLOS ONE (I was a co-author), so I invited him to write up a post for the blog. — A. Farke

Anatomical and behavioral differences distinguish males and females in many extant and extinct animals. For instance, male peacocks have a large and flashy tail, whereas females are smaller and less brightly colored. Male lions have a mane and are larger than females. Red deer male sport antlers, lacking in females. This phenomenon is called sexual dimorphism and represents a product of sexual selection. It represents a key factor in the success of breeding within many species, as originally stated by Darwin, and mate choice.

Peacock (back) and peahen (front), in a classic example of sexual dimorphism. Image by Darkros, in public domain.

Peacock (back) and peahen (front), in a classic example of sexual dimorphism. Image by Darkros, in public domain.

Despite obvious sexual dimorphism in some modern animals, sexual dimorphism is hard to identify in extinct organisms such as dinosaurs, often due to a very small sample size. Having a few fossil skulls with different morphologies (crest or horns) and relating them to sexual differences thus appears quite hasty. For instance, hypothesized males and females of hadrosaurs (Parasaurolophus or Lambeosaurus) were later shown to be species separated in time and in space. Variation in the number of chevron bones (wishbone-shaped bones under the tail vertebrae) in Tyrannosaurus, previously attributed to sex differences between males and females, are instead the product of non-sexual variation.

Ceratopsians, popularly known as “horned dinosaurs”, represent another group for which paleontologists have inferred sexual dimorphism. Protoceratops andrewsi is a well know ceratopsian from the Late Cretaceous of the Gobi Desert, Mongolia, discovered almost a century ago during the American Museum Expeditions of the 1920s. Protoceratops is a small (<2 m total body length) quadrupedal animal, characterized by a skull with a thin, bony frill projecting over the neck and lacking the prominent horns that characterized ceratopsids such as Triceratops. More than one hundred well-preserved skulls and skeletons (many from various life stages) have been unearthed, providing a lot of information on its paleoecology and paleobiology. This large sample size allows a statistical test on whether shape differences of skulls could be truly related to sex.

Variation in Protoceratops skulls; the skull on the left has been previously hypothesized as male, whereas the skull on the right has been suggested as female. Scale bars equal 10 cm. Image from Maiorino et al. 2015, modified from original by Brown and Schlaikjer 1940.

Variation in Protoceratops skulls; the skull on the left has been previously hypothesized as male, whereas the skull on the right has been suggested as female. Scale bars equal 10 cm. Image from Maiorino et al. 2015, modified from original by Brown and Schlaikjer 1940.

Back in 1975, Peter Dodson used skull measurements from 24 specimens to investigate growth changes in Protoceratops as well as possible sexual dimorphism. He assigned the sex to each specimen on the basis of its position on scatter plots (above or below a trend line). Based on this analysis, Dodson hypothesized that male Protoceratops had a broader and taller frill, broader skull above the eyes, and taller nasal bump than seen in females. This analysis was quite advanced for its time, but given advances in statistical methods, morphometrics, and computing power, as well as the discovery of many new fossils, we decided to look at the problem again.

Geometric morphometrics is a suitable method to analyze shape and size differences among groups of animals. Where previous work used basic measurements, we digitized the shape of 29 skulls in top and side views, based on photographs. We assigned skulls to male or female using the previously outlined criteria. Geometric morphometrics allows the study of shape variation within sampled specimens and capturing the overall geometry (instead linear measurements) of biological structures by means of simple analyses. How can we detect shape information? It is easy: just digitizing spots on images (called landmark) on homologous anatomical features for the all skulls (in our case) in top and side view. By so doing, we have now a large sample constituted by geometries that represent the shape of the skull.

We asked ourselves, if males and females have different skull shape, are we able to distinguish the two groups using geometric morphometrics and statistical tests?

We plotted all specimens in a X-Y graph. One graph for the Protoceratops individuals in side view, and one other for the individuals in top view. We refer to those X-Y graphs as “morphospace” because they represent the shape variation of the specimens in the space. Those two graphs highlighted that males and females overlap each other; the two groups are not well separated in the plots. This suggests that males and females possess similar skull shape. Moreover, we used statistical tests to verify if what we can see in the graphs is statistically reliable and thus if the shape difference between males and females is well-founded.

Note the overlap between "male" and "female" Protoceratops; if there is sexual dimorphism, it is fairly week. Image from Maiorino et al. 2015.

A plot of morphospace for Protoceratops skulls in side view. Note the overlap between “male” and “female” Protoceratops; if there is sexual dimorphism, it is fairly weak. Image from Maiorino et al. 2015.

No matter how we plotted or analyzed the data, we weren’t able to find a clear, statistically significant difference between males and females. Therefore, we think that the previously hypothesized criteria are not suitable to distinguish the two sexes in Protoceratops andrewsi easily. Frill height and width as well as the width of the skull over the eyes do not represent sex-discriminant features in our sample. The occurrence of the horn above the nose would seem partially related to sexual dimorphism, even if this evidence is not well-rendered.

We suggest that cranial shape variation previously interpreted as sexual dimorphism is related instead to shape changes occurring during the animal growth and perhaps also related to the shape variation occurring among the adults of this ceratopsian dinosaur. Maybe, new fossils will give the chance to confirm our results or reject them.

Citation
Maiorino, L., A. A. Farke, T. Kotsakis, and P. Piras. 2015. Males resemble females: re-evaluating sexual dimorphism in Protoceratops andrewsi (Neoceratopsia, Protoceratopsidae). PLoS ONE 10:e0126464.

Category: Dinosaurs, Paleontology, PLOS ONE, Zoology | Tagged , , , , | Comments Off on Guest Post: Can We Easily Distinguish Male and Female Protoceratops?

International Museum Day

Today is International Museum Day. Today (and every day) I’m grateful for museums and the people who work in them. Natural history museums (especially The Field Museum in Chicago) were key inspirations that got me on my path to a career in evolutionary biology. It’s no stretch to say that museums helped make me who I am today – they opened my eyes to the amazing planet we live on and got me excited to learn about it. More than any teacher, museums encouraged me to explore the world and to add to our understanding of it.

The Field Museum inspired me to become a scientist.

The Field Museum inspired me to become a scientist.

Perhaps because of this, I think about museums as an equalizing force. A leg up for kids who weren’t born into money. A path to change. Just 150 years ago, most museums were private, essentially curio cabinets for wealthy people to display their collections. The idea of museums as a public good –that the beauty and wonder of the world should be accessible and inspiring to all– is one of the great cultural advances we have seen in that time.

Museums preserve our natural and cultural heritage, remind us of humanity’s greatest achievements and its lowest moments. They expose us to beauty and darkness, and challenge our assumptions about ourselves and others. Like all educational institutions, museums are a democratizing force. Their very existence proves that the world is bigger than our particular circumstances, that there are better things out there than what we observe from day to day, and that there are other ways of doing things than those we were taught.

Museums are powerful; they give us hope, question the status quo, and inspire us to be better versions of ourselves. This really is a revolutionary concept; if these ideas weren’t threatening, the existence of museums would never be at risk. Invading forces wouldn’t destroy them when they took over new area. Politicians would not be so keen to defund them.

So, today (and every day), I encourage you to support and protect your local, state, and national museums. Visit, volunteer, and become a member. Donate to funds that get kids in the door. Combat their defunding. Don’t elect politicians or school boards who think museums aren’t valuable. Support school districts, principals, and programs who advocate student access to museums. Museums preserve our past, but they also have the power to change the future.

Be like Patrick. Support museums.

Be like Patrick. Support  museums. Become powerful.

Category: Miscellaneous, Museums, Navel Gazing, Uncategorized | Tagged | Comments Off on International Museum Day

Sharing Paleodata (Part 4): MorphoSource

Today I continue my series highlighting repositories for paleontological raw data. Previous posts in this series can be found here, here, and here.

 

Welcome to the MorphoSource

MORPHOSOURCE (http://morphosource.org/)

MorphoSource is a data repository for 3D data – raw CT and microCT data, but also surface models, slice movies, and 2D images. It’s the brainchild of Doug Boyer, an Evolutionary Anthropology professor at Duke. While there are plenty of data repositories for 2D images (e.g., MorphoBank and MorphBank), there really isn’t an equivalent for raw 3D data. Yes, some sites like Dryad or Figshare can host CT datasets (as Andy and I did for our 2013 “Dinosaur Joe” paper), and the website DigiMorph hosts these data in a more limited format, but currently there’s no dedicated repository for raw CT data.

CT has been an increasingly common tool in paleontological research for the last two decades, but for most of that time, CT datasets were too large to host online. Early on, Tim Rowe and his UT Austin colleagues set up DigiMorph as a central online repository for hosting the data, albeit in smaller file formats. DigiMorph has long been the only site focused on paleo/morphology CT data; they currently host an impressive 1ooo+ datasets. I’m a big fan of DigiMorph and use it regularly in both teaching and research, but it has some limitations. First, nearly all of the DigiMorph data comes in video form (movies that cycle through CT slices or show spinning rendered volumes) or annotated 2D images. Only ~50 have associated downloadable STL files (surface meshes/models), and none of the raw data (projections or slices) are downloadable. There’s also a backlog of specimens that have yet to be uploaded, because they only have so many techs and they all have many other responsibilities. MorphoSource answers these concerns by allowing users to upload their own raw data and STL files, in addition to movies and 2D images.

Full Disclosure: The statements about MorphoSource in the “Nitty Gritty” section were checked for accuracy by Doug Boyer (site director). The impressions are my own. I’ve used the site for a couple months now, and have submitted, shared, viewed,  and downloaded data.

 

Lemur tooth

3D surface mesh of a ring-tailed lemur molar. Image from: http://morphosource.org/index.php/Detail/MediaDetail/Show/media_id/307

 

Impressions: Two weeks ago, University of Texas sent me some fossils. I opened the box on Wednesday night, photographed and measured my specimens on Thursday, and on Friday morning at 7:30AM, I scanned all 8 bones. By noon, I had made some surface meshes in Avizo, created a MorphoSource project, uploaded all the dicom and STL files (the raw data and my interpretations of it), and shared the whole shebang with the collections manager. In two days I went from a sealed box to having returned all the data to the lending institution. Yes, it’s highly unlikely that anyone will need to see this particular right femur of a juvenile false gharial in the few months I have these guys on loan, but if they do, Texas already has the data and a surface model they can share with people who need it. So, yeah, I really like MorphoSource and find it beneficial even prior to publishing anything publically on the site. It’s now my go-to site for 3D data management.

Part of its appeal is that it sticks to functionality and doesn’t get bogged down in unnecessary features – no social media stuff; it’s all business and functionality. In several months of use, I’ve never had problems with the site; no crashes, stalled downloads, or errors. I was able to figure out the site without needing to consult the User Guide, although it took me a couple hours to become comfortable navigating and uploading. If I had read the directions first, I probably wouldn’t have found some aspects clunky (see below), because I would have anticipated what information I needed to have on hand before uploading.

To begin, you create a project, and then add taxa and specimens before uploading media files. It auto-searches to see if someone has previously entered a taxon or specimen number, which is pretty handy. You determine who can view/download the media before the project is published by adding collaborators. Collaborators can see all specimens within a project, but you can also choose to share a given specimen with people outside your collaboration group (if you didn’t want to give them access to every specimen). Outside of collaborators, nobody can see your data until you publish it. Upon publication, you can decide whether everyone can download it without contacting you, or if they need to email you for permission before access is granted. You can also elect to be notified passively when people download your data. After publication, people can view your surface meshes in the browser, but if they want to download data, they need to register to do so.

So far, I’ve included collections managers as collaborators on projects that involve their museum’s specimens. One nice feature: if I want to, I can give them sole access to the project/media/specimen (i.e., transfer the project to them) after publication. I like this idea a lot; most museums ask for the raw CT data upon publication anyway, and this is a good way to both give them the data and allow them to control and track its use down the road.

In addition to sharing the tiff or dicom stack, you can also share movies and surface meshes, duplicating a major and minor feature of DigiMorph, respectively. An especially helpful tool is the ability to view and rotate surfaces in-browser, without having to download the file or requiring sophisticated 3D software. This has already proved useful in sharing data with my colleagues; they can view and manipulate the specimen virtually while we chat about it over the phone. As a tool for real-time collaborative research, this is pretty great. It also has a lot of promise as an outreach and education tool – for example, the Florida Museum of Natural History has uploaded surface meshes for two K-12 educational projects on Horse Evolution and the megasnake Titanoboa. I can see MorphoSource as a great supplement for in-class activities or virtual lab assignments; for example, using this incredible dataset of primate skulls in the Harvard MCZ collection.

3D surface mesh viewer

Screenshot of the 3D surface mesh viewer

If you want “official” credit for these open-data efforts, you can request a DOI for projects or media items. The first time, you’ll need approval as a DOI user and then it’s a simple request each time you need a DOI after that.  They’ve also included some pretty cool features that make downloading files and managing metadata easier. If a large dataset is available for immediate download, you can choose specific specimens to download using a shopping cart button. Once you get to the “check out” page, you can opt to download only part of the data, say, only the meshes or tiff stacks. You can also download all the metadata for every specimen in your cart as a CSV – all the specimen data and scan parameters in one file, so you don’t have to hunt for the information later.

Another strong positive is Doug Boyer himself. I’ve been testing the site for a couple months now, and have sent him several suggestions by email. Each time, he took the time to read and respond, indicating which were already planned, which weren’t practical, and which were good ideas. Some of these have already been incorporated. He’s really invested in the functionality of the site, and wants to ensure that every feature directly relates to the primary goals of storing and sharing data.

There aren’t many negatives. I find searching a little clunky (they’re working on improving this), but browsing is ok once you get used to using in-window forward and back arrows to navigate. Initially I thought it was a little annoying to have to enter and save taxonomy, specimen, and scan information before uploading can begin, but really, it’s no more cumbersome than the same process on MorphoBank. One advantage over MorphoBank is that basic museum, specimen, and taxonomic information are accessible to the whole site once one person enters it – nobody will ever have to go through the trouble of entering the higher taxonomy of Tomistoma schlegelii again. Currently, each specimen requires entering a genus and species, which for my critters is not always possible (my best workaround is entering g: Phytosauria, sp: indet, or g: Incertae, sp: sedis). Future improvements will include the ability to search using higher taxonomy, which will get around this problem to some extent.

Bottom Line: MorphoSource is functional and fairly easy to use. Currently, it’s probably the best option for sharing raw CT data. Grant writers should feel comfortable listing MorphoSource in their Data Management Plan. Reviewers should feel comfortable asking authors post data to MorphoSource.

 

A Titanoboa vertebra used in a K-12 project published on MorphoSource.

3D surface mesh of a Titanoboa vertebra, published as part of an education/outreach project aimed for K-12 teachers and students. Image from: http://morphosource.org/index.php/Detail/MediaDetail/Show/media_id/5943

 

MORPHOSOURCE: THE NITTY GRITTY

What it is: 3D data repository for CT and microCT data

What it is, in their words: “a project-based data archive that allows researchers to store and organize, share, and distribute their own 3D data”; also “an image-sharing resource designed to allow users to upload, search, and browse high quality 3D images”

Who runs it: Doug Boyer, Duke University

Who funds it: Duke University (directly and by hosting the site), NSF (BCS 1317525; BCS 1304045)

Who uses it: Researchers who use, download, or submit 3D data.

Cost to submit: Free (registration required).

Cost to access: Free (registration required to download).

Data and file types supported: 2D images: JPEG, PNG, TIFF, DICOM and PSD. Video: MPEG-2, MPEG-4/H.264, FLV, QuickTime, and Windows Media. Surfaces: PLY and STL. You can also submit zipped archives of TIFF and DICOM files. I included Avizo files within my zipped archive with no uploading issues.

File sizes allowed: No limit

Copyright status: You choose whether or not the data is copyrighted and who owns the copyright. You select among Creative Commons licenses (CC0 and CC/BY/NC/SA/ND) or release the data for one-time use on MorphoSource. No option (yet) to upload a copyright permissions document, but you can copy text from those documents into the notes. Nifty feature: you can opt to receive a notification email when your data are downloaded, or require users to contact you for permission before data are downloaded.

Data available during peer review? Kinda, in that you can make the data live at submission rather than upon publication of the paper.

Allowed to post data from previous pubs? Yes, even publications published before MorphoSource existed, and they invite and encourage this practice.

Accession numbers provided? Every project, specimen, and media item gets their own accession number (similar to GenBank) as you upload them. You can also request a DOI.

Data goes live when: You choose to publish the project. Data can stay as an unpublished project forever, or you can publish it when you like – before or after the manuscript is accepted, when embargo is lifted, when the paper is published, etc.

Data is backed up? There are 4 copies (RAID1 drives in 2 separate physical locations). Currently applying for funding to expand physical storage, add additional cloud storage, and expand the archival system.

Stats provided? Number of views and downloads for each specimen and media item. You can also see which registered users have viewed/downloaded your files.

How to cite your data in your manuscript? Cite the MorphoSource software. Right now there are two extended abstracts (Boyer et al. 2014; Kaufman & Boyer 2014 , but there’s also a formal paper in the works

Boyer DM, Kaufman S, Gunnell GF, Gomes E, and Thostenson J. 2014. MorphoSource: A currently active project-based 3D digital web-accessible data archive for museums and individuals at Duke University USA. In: Mallison H, Vogel J, and Belvedere M, editors. Digital Specimen 2014 – Abstracts of Presentations. pp 8-12.

Kaufman S, and Boyer DM. 2014. Developing Platforms for Management and Distribution of Digital Specimen Data. In: Mallison H, Vogel J, and Belvedere M, editors. Digital Specimen 2014 – Abstracts of Presentations. p47.

You should also cite your data, something like: “TIFF stacks and STL files are available on MorphoSource (http://www.morphosource.org): Project XXX (DOI: ). Media accession numbers are listed in Table X.”

How to cite data you download from someone else’s project? DOI, if they have one. Otherwise cite the site, project and media numbers.

Can update after publication? Yes. In their words: “You always have the option of removing materials from public view, and adding new media to longstanding projects.” *This may not be the case for DOI-assigned media.

Benefits in a nutshell:

  • Secure cloud storage of 3D surfaces and raw microCT and CT scan data
  • Accessible to your collaborators before publication
  • View and rotate 3D surface meshes in your browser
  • Add new citations to a project as you/others re-use the data
  • Notification when people view/download your dataset
  • You can require people to ask permission before downloading data

Three recent paleo papers using it:

Evans, SE, JR Groenke, MEH Jones, AH Turner, DW Krause. 2014. New material of Beelzebufo, a hyperossified frog (Amphibia: Anura) from the Late Cretaceous of Madagascar. PLoS ONE 9(1): e87236. MorphoSource data example: media S1312, a presacral vertebra. YOU CAN DOWNLOAD YOUR OWN BEELZEBUFO, PEOPLE!

Chester, SGB, JI Bloch, DM Boyer, WA Clemens. 2015. Oldest known euarchontan tarsals and affinities of Paleocene Purgatorius to Primates. PNAS 112(5): 1487-1492. MorphoSource data example: media S1405, an astragalus.

Boyer, DM and ER Seiffert. 2013. Patterns of astragalar fibular facet orientation and their evolutionary implications in extant and fossil primates. American Journal of Physical Anthropology 151(3): 420-447. MorphoSource data example: media S1083, a different astragalus.

Category: Digitization, Open Data, Paleontology | Tagged , , | 4 Comments

Romer’s Gap and the Four-Limbed Critters of Nova Scotia

The fossil record is a window into the past, but much of that window is boarded over. This situation spurs paleontologists to look in new places and new rocks, in an attempt to pry some of those boards off that window into our planet’s history. This is a great example of how paleontology is a testable science. Missing fossils from a certain time span? Look in rocks from that time span, and you should find them!

Romer’s Gap” presents a classic case of the incomplete fossil record. We know quite reliably that tetrapods–the four-limbed vertebrates including amphibians, reptiles, and us–originated around 370 million years ago. Fossils from 365 million years ago show distinct arms, legs, fingers, and toes on animals such as Acanthostega, leaving no doubt as to their tetrapod status. And we also know that tetrapods were pretty successful after that, because I’m using my tetrapod forelimbs (arms, hands, and fingers) to type out this blog post. But frustratingly, a time slice from around 360 to 345 million years ago yields precious few tetrapod fossils. This phenomenon was first noted by paleontologist Al Romer, hence its nickname of “Romer’s Gap“. The gap frustrates scientists because it is so soon after the origin of tetrapods, immediately before many important groups appear in the fossil record. That interval probably includes many events central for the transformation of tetrapods from leggy fish into truly terrestrial organisms. Tetrapods must have been around during Romer’s Gap, but where were they?

Romer's Gap is a ~15 million year interval, during which a whole bunch of tetrapod evolution presumably happened. Sites such as Blue Beach help to fill this gap. Eoherpeton at top modified from original by Nobu Tamura (CC-BY). Ichthyostega at bottom modified from public domain original by Scott Hartman.

Romer’s Gap is a ~15 million year interval, during which a whole bunch of tetrapod evolution presumably happened. Sites such as Blue Beach help to fill this gap.
Eoherpeton at top modified from original by Nobu Tamura (CC-BY). Ichthyostega at bottom modified from public domain original by Scott Hartman, phylopic.org.

Various ideas have been proposed to explain the gap. Two front runners include:

  • Low atmospheric oxygen levels put a damper on land animals. No oxygen, no animals. But, it turns out that oxygen wasn’t that much lower than other times in history, and were actually higher than times just before the “gap”. Furthermore, marine waters should have had even lower oxygen (long story–I’ll just wave my hands and say “Chemistry!”), providing extra pressure for tetrapods to move onto land.
  • Artifact of collection and/or preservation. Is there a genuine gap in the fossil record? For any number of reasons, the fossil record is patchy. You might not have rocks from the type of environments to preserve particular organisms, or paleontologists just haven’t gotten around to studying the appropriate rocks yet.

As more paleontologists seek out more fossils, the latter hypothesis is starting to gain ground. A new study by Jason Anderson and colleagues, just published in PLOS ONE, provides additional support along these lines.

Rocks from the Horton Bluff Formation in Nova Scotia that yield fossils filling "Romer's Gap". CC-BY, modified from Anderson et al. 2015.

Rocks from the Horton Bluff Formation in Nova Scotia that yield fossils filling “Romer’s Gap”. CC-BY, modified from Anderson et al. 2015.

Blue Beach, rimming an estuary on the Bay of Fundy, has a long history of producing fossils from the time span including the base of Romer’s Gap. But, these rocks are notoriously hard to work. Wide swings in tidal levels limit working time to only a few hours a day, and most fossils are isolated bones difficult to assign to a particular kind of animal. Unless the finds are collected soon after exposure, they are lost to wave action. Thankfully, discoveries by local amateur paleontologists, in concert with fieldwork by external researchers, have slowly and steadily produced a stream of fossils.

The fossils described in the new study are nearly all isolated bones–individual limb, pelvic, and shoulder girdle pieces. But, by comparing them to more complete finds from elsewhere, it is possible to identify the specimens to varying degrees of precision.

Humerus (arm bone) of an early tetrapod from the Blue Beach locality. CC-BY, from Anderson et al. 2015.

Humerus (arm bone) of an early tetrapod from the Blue Beach locality; multiple views of the same fossil. CC-BY, from Anderson et al. 2015.

Let’s face it–the limb bones of early tetrapods are pretty clunky objects, lacking the sweeping and elegant lines of today’s salamanders, lizards, or mammals. The above image is a great example of a typical early tetrapod arm bone. But, each awkward ridge and bump points to the bone’s original owner. For instance, the bone shown here is similar to that of an animal called Pederpes, which belongs to a family of early tetrapods called Whatcheeriidae. Imagine something that looked like an ugly salamander, and you’ve got Pederpes.

All together, 37 different specimens (including isolated limb bones, skull bones, and even a handful of specimens with multiple bones from the same individual) were studied by Anderson and colleagues. The fossils could be referred to six or seven different groups of early tetrapods, showing that tetrapods were going strong even in the middle of Romer’s Gap. Some of these (closely related to Ichthyostega, shown below) are forms that are most closely associated with earlier times in earth’s history; one way or another, they made it through a big extinction just prior to Romer’s Gap. Maybe, then, the extinction didn’t hit tetrapods as hard as previously thought.

An ominous Ichthyostega. Silhouette by Scott Hartman via phylopic.org, public domain.

An ominous Ichthyostega. Bones from a closely related animal were found at Blue Beach. Silhouette by Scott Hartman via phylopic.org, public domain.

Blue Beach isn’t the only locality to plug Romer’s Gap–another recently described set of fossils from Scotland shows a similarly rich tetrapod ecosystem. Together, these localities in disparate parts of the world suggests that the purported gap in the fossil record is more a collecting artifact than the result of genuine rarity of these animals during their time. Anderson and colleagues perhaps summarize it best:

“It now seems that, whenever we discover rare windows into this time period, we find numerous fossil tetrapods reflecting a rich diversity of forms.” — Anderson et al. 2015

In other words, Romer’s Gap probably isn’t a real phenomenon! With more fossils, it’s getting shorter and shorter. This is so often the case in paleontology–and that’s a good part of what keeps us all out looking for fossils. A “gap” in the fossil record is just a challenge to overcome.

Citation
Anderson JS, Smithson T, Mansky CF, Meyer T, Clack J (2015) A diverse tetrapod fauna at the base of ‘Romer’s Gap’. PLOS ONE 10(4): e0125446. doi:10.1371/journal.pone.0125446

Category: Paleontology | Tagged , , , | 6 Comments

Brontosaurus thunders back!

Pretty much every person who ever read a dinosaur book or went to a natural history museum learned that Brontosaurus is just an outdated name for a big long-necked dinosaur that should be called Apatosaurus. Two different names were applied to the same type of animal, but Apatosaurus wins out because it was named first.

But…it’s just not that simple. It’s never that simple! In a move that is sure to generate considerable discussion by scientists and non-scientists alike, Brontosaurus is back. This topic is being covered in immense detail by many other writers, so I’m going to give just a quick tutorial here. In the interests of full disclosure, I should also note that I was the volunteer editor who handled this paper for the open access journal PeerJ. The opinions expressed here are solely my own.

An old school Brontosaurus, as envisioned in the late 1800s. After Marsh 1896.

An old-school Brontosaurus, as envisioned in the late 1800s. After Marsh 1896.

So, how do we resurrect Brontosaurus? It’s not just a matter of arbitrary scientific opinion–the authors of the new study, Emanuel Tschopp, Octávio Mateus, and Roger Benson–didn’t wake up one morning and say, “Hmm…let’s mess with people.” The work entailed a ridiculously awesome amount of hands-on study of specimens around the world, as well as detailed analysis of the features of the fossils to determine their evolutionary relationships.

Evolutionary relationships are the key–erecting, demolishing, or maintaining species and genera requires an understanding of how these organisms are related. Basically, if species of Brontosaurus are all mixed in with species of Apatosaurus, then the two animals should be recognized under one name (Apatosaurus). If, on the other hand, what used to be called Brontosaurus is evolutionarily well separated from species of Apatosaurus, then Brontosaurus stands up.

In order to see how the species are related, Tschopp and colleagues built a massive database documenting the anatomical features for numerous relatives of Apatosaurus–at the individual specimen level. This was the largest-scale study of its type ever done; most other studies (with few exceptions) have lumped specimens together under species, or have lumped species together into genera. A fine-scale approach, looking at individual specimens, turns out to be key. Once all of the specimens were coded, they were subjected to a phylogenetic analysis to determine which possible evolutionary trees best fit the data. In other words, a computer algorithm took the data and found which possible arrangement of evolutionary relationships made the most sense in light of the anatomical evidence. Animals that share more features changed from the ancestral condition (“derived features” in paleontological parlance) are assumed to be more closely related.

In the diagram below, which is roughly similar to a previously published analysis by Paul Upchurch and colleagues, note that the original Brontosaurus species (Brontosaurus excelsus) is in the middle of a whole bunch of Apatosaurus. Species more closely connected are more closely related–and here, the original Brontosaurus species is more closely related to the original Apatosaurus species than anything else. Unless one wanted to name each of those other species its own genus (a practice  employed for many other dinosaur groups), it made the most sense to keep Brontosaurus the same as Apatosaurus.

Tentative evolutionary tree of Brontosaurus and Apatosaurus

A hypothetical  view of the evolutionary relationships of Apatosaurus and Brontosaurus, based in part on a previously published analysis by Upchurch and colleagues. The dates at right indicate when each species was named. If this arrangement is correct, then Brontosaurus should be called Apatosaurus.

In their own analysis, Tschopp and colleagues found that Brontosaurus excelsus is well separated from the two species most traditionally considered Apatosaurus. Not only does the shape of the evolutionary tree show this, but the sheer quantity of differences also supported Brontosaurus as something different from Apatosaurus. By the paper’s standard of a “genus”, Brontosaurus fits the bill.

A new evolutionary hypothesis showing Apatosaurus and Brontosaurus as different genera.

In this arrangement, based on that found by Tschopp and colleagues, Apatosaurus and Brontosaurus are two different genera. As an interesting side-note, Brontosaurus parvus originally got its own name, Elosaurus. But, because it is “nested” within Brontosaurus, it keeps that name. As another side-note, Brontosaurus yahnaphin has also been called Eobrontosaurus. So, one could make an argument that BrontosaurusElosaurus, and Eobrontosaurus are all valid! This is where things can get a little subjective, but Tschopp et al. posit that the differences are few enough so that they should also be Brontosaurus.

So, Brontosaurus lives again! In terms of pop cultural significance, this is a pretty big deal–but in terms of scientific nomenclature, these kinds of things happen all of the time. In fact, the real treasure of the paper by Tschopp and colleagues is its in-depth approach to unraveling the evolutionary relationships of ApatosaurusBrontosaurus, and their relatives. This level of detail is becoming increasingly common for dinosaur research, and as demonstrated here can be a pretty handy tool for unraveling long-standing problems in identifying and naming species.

Brontosaurus has an unparalleled hold on the public imagination–its name aptly means “thunder lizard,” after all. As such, it’s a prime example for showing how scientists classify and reclassify organisms in light of new information.  Papers such as this, beyond taking care of naming species and genera, provide an important backbone for other analyses. If we want to understand the migrations and interchanges of dinosaurs between continents, we have to know how the various species are related. If we want to correlate the origination or extinction of species to climate changes or other global events, we have to have a solid grasp on these same relationships. Scientific progress thunders onward!

Citation
Tschopp E, Mateus O, Benson RBJ. (2015) A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda) PeerJ 3:e857 https://dx.doi.org/10.7717/peerj.857

[post edited to add clarification on shared derived features, add links to other blog posts, fixed a typo or two]

Category: Dinosaurs, Paleontology | Tagged , , , , | 4 Comments