A TEXT POST

Cervical ribs in mammals - why it matters

Last month, we published “Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths”, which received quite a bit of attention in the press. In this article, Frietson Galis and her group describe the presence of a cervical rib in Woolly mammoths providing some clues about their decline and eventual extinction.

We felt it would be informative to ask Dr Galis how she became interested in cervical ribs in mammoths. She told us that she was in fact interested in cervical ribs in all mammals!

Such a rib is attached to the seventh vertebra and this signifies a change of the normally extremely constant number of neck vertebrae from 7 into 6. Giraffes with long necks have 7 neck vertebrae and the short-necked dolphins also. Ribs are normally only attached to thoracic vertebrae and the presence of a rib on the seventh vertebra indicates a change of identity of a neck vertebra into a thoracic one. Study of exceptional mammals with an aberrant number of neck vertebrae has taught us that this change almost unavoidably comes with side effects and congenital anomalies. Thus, finding cervical ribs is always interesting for me and in the case of the Woolly mammoth it is extra exciting, as it provides us with unexpected insights into their condition before getting extinct.”

Dr Andrew Farke (Academic Editor on this article) also thinks this study generates some cool ideas to test. “This work is interesting because it uncovers a neat potential line of future research—developmental anomalies in animals under environmental stress”, he said. “Although this type of work is still in its infancy, I am excited to see how it develops. I do wonder if these sorts of anomalies can be used in studies of contemporary animals, too—perhaps for species of strong conservation importance”.

We couldn’t agree more with Dr Farke, and also hope that in the near future more researchers will use fossils to study developmental pathologies.

We encourage you to check out some of our other paleontology publications in PeerJ.

A TEXT POST

Live Event - ‘Ask Me Anything Journal Club’ with the Dino Joe authors

We are pleased to announce that this Wednesday, 13th November, from 8 am – 10 am PST (4 pm – 6 pm UK time) two of the authors of the recent ‘baby hadrosaur’ (‘Dino Joe’) article will be online and fielding questions on any aspect of their article, or of their work in general. This is your chance to find out how paleontology is performed in the open science era, and to ask Andy Farke and Sarah Werning anything at all. Yes - anything!
 
For this live event visit https://www.peerj.com/ask/dinojoe/. Your questions can be left at any time - before, during or after the event - and the authors will be online and interacting on Wednesday. As the ‘questioner’ you are able to ‘accept’ any answer (indicating that it sufficiently answered your question) and any participant can vote answers up or down as they wish.

image

Fig 6 - Reconstruction of the skull of Parasaurolophus sp..
 
So mark your calendar, and visit https://www.peerj.com/ask/dinojoe/ from 8 am PST on Wednesday to interact with Andy Farke, Sarah Werning and Dino Joe.

A TEXT POST

The Reception to Dino Joe

On Tuesday, we published Ontogeny in the tube-crested dinosaur Parasaurolophus (Hadrosauridae) and heterochrony in hadrosaurids” by Dr. Andrew Farke et al.

This fascinating paper describes the most complete skeleton ever found of Parasaurolophus, a duck-billed and plant-eating dinosaur. It’s also the youngest: The fossil is a rare baby dinosaur, under a year old when it died 75 million years ago. It got a lot of great coverage including spots on NBC LA, CCTV, Utah Public RadioSlate, Nature Magazine, Science Magazine, The Guardian and many others.

image

With well over 20,000 views of the peer-reviewed paper (in the first 3 days alone), and over 100,000 visitors to the museum’s custom web-site, this is already the most read paper that PeerJ has published, and is clearly one of the most accessed (as well as accessible) paleontology discoveries ever. This publication is a testament to the power of open access, and so it was great timing to have published it in Open Access Week.

Given the broad attention the article generated, we asked Dr Farke to tell us in his own words about his incredible, but tiring, week.

AF: “What happens when you publish the world’s most open access dinosaur? Pure pandemonium!

On Tuesday, my co-authors (recently graduated high school students Derek Chok, Annisa Herrero, and Brandon Scolieri, along with paleontologist Sarah Werning) and I published a paper in PeerJ describing the nearly complete skeleton from a baby Parasaurolophus. Beyond the “gee-whiz” factor of a dinosaur fossil (found by another high school student!), the specimen nicknamed “Joe” tells us a whole bunch about how an iconic plant eating dinosaur grew some bizarre headgear. We also decided to make this the most open access dinosaur ever—not only was the paper published in an open access journal, but all of the digital scans and imagery were archived to Figshare. Although parts and pieces of digital scans had been made public for other fossils, this was the most comprehensive dataset yet available for any dinosaur. Because these sorts of scan files aren’t necessarily easily accessible to the general public, we set up a website (www.dinosaurjoe.org), so that anyone could view the fossil from all angles in 3D without the aid of specialized software.

Of course, we wanted to let people know that an open access dinosaur had arrived! We crafted a press release and sent it out the week before publication, and waited. And waited. I was a little worried that we had sent it out too soon, or that it had landed without a sound.

Fortunately, those worries were unfounded. By the time that the publication date rolled around, things were completely out of control! The phones at the museum were ringing off the hook, television trucks were lined up on the road outside the exhibit hall, and over 100,000 visitors saw the specimen on-line. It was a fantastic day for our museum, our school, and open science.

On a personal level, I am proud of the results of the efforts of everyone involved. Kevin Terris, the high school student from The Webb Schools who found the fossil, rightfully received global recognition for his incredible find. Brandon Scolieri, Derek Chok, and Annisa Herrero, the three Webb students who helped write the paper, did an incredible job on their specific research focuses. Sarah Werning's work on bone tissue allowed us to estimate the age of the dinosaur, adding critical context to the study. This all added up to a comprehensive paper. And most of all, I am proud of how open the study is! It is truly amazing to be able to share this fossil with the world, so completely. PeerJ helped this happen!

Two things really capped this experience for me. The first was seeing the well-deserved congratulations pour in for Kevin Terris on his discovery. This is not his last major find, and I am also excited that a paper he co-authored during his time at Webb will be published before the end of the year! The second highlight of this week was a set of comments from Ben Richmond, writing about the open access angle of the find for The Motherboard blog at Vice.com:

"It allows people like me who never get to touch dinosaur skeletons, even if we really want to, to spin Joe around and look at him up close from any angle we want…If this is the future of museums, museums [are] going to be awesome for a long time."

For those of us who want to share our fossils with the world, can it get any better than this?”

Dr. Andy Farke

image

The skeleton of “Joe” the baby Parasaurolophus ready to meet the public. CC-BY, by Andy Farke.

A TEXT POST

Guest Post – Dr. Andrew Farke and his Baby Dinosaur

Today, PeerJ is pleased to publish the work of Dr. Andrew Farke, and his group, in their article Ontogeny in the tube-crested dinosaur Parasaurolophus (Hadrosauridae) and heterochrony in hadrosaurids.

This article describes the most complete skeleton yet known from an iconic dinosaur (the hadrosaur, or “duckbilled dinosaur”, Parasaurolophus), with preserved rare skin and beak impressions. The fossil is a rare baby dinosaur, under a year old when it died 75 million years ago. Study of the skeleton revealed that the hadrosaur formed its unusual headgear by expanding its skull bones earlier and for a longer period of time than did its close relatives.

Because of the broad importance of the finding, researchers have made 3D digital scans of the entire skeleton accessible. It is the first time that virtually an entire skeleton has been made available via open access for anyone to use and reuse.

Dr. Farke, lead researcher on the study and corresponding author on the manuscript, received a B.Sc. in Geology from the South Dakota School of Mines and Technology in 2003, and completed his Ph.D. in Anatomical Sciences at Stony Brook University in 2008. He joined the staff at the Alf Museum in June 2008, as Augustyn Family Curator of Paleontology.

He wrote the following guest post, giving us some details concerning the study of the fossil and the reasons why he decided to submit the findings to PeerJ.

image

AF: “It’s a long road to travel when a spectacular fossil noses its way out of bedrock and into your museum. In this case, it was the nearly complete skeleton of a baby dinosaur, found by Kevin Terris, a high school student back in 2009. My museum— the Raymond M. Alf Museum of Paleontology—is on the campus of a high school (The Webb Schools), and we take students out in the field with us every year. The first question is, how do we get it back home? Following a flurry of excavation permits (from Bureau of Land Management, Utah, and Grand Staircase-Escalante National Monument, who manage the land the fossil was found on), two weeks of excavation, and a helicopter flight, the specimen was in a truck on its way to our museum. A year and a half of preparation painstakingly peeled the rock away from the fossil bones, and then it was time to begin the research.

A fantastic crew of researchers joined the project—Derek Chok, Annisa Herrero, and Brandon Scolieri (three high school students from The Webb Schools) as well as Sarah Werning, a paleontologist and bone biologist. We swiftly went to work, trying to extract as much data from the fossil as possible. Detailed study of its anatomy revealed that the six-foot long skeleton belonged to a baby Parasaurolophus—the iconic tube-crested plant-eater that lived throughout western North America around 75 million years ago. Even though the animal was less than a third of its full adult size, it had already sprouted the rudiments of the crest that makes the dinosaur famous. Medical CT scans revealed well-developed nasal passages, which may have been used to trumpet calls to other members of its species at a pitch far higher than the low, booming calls of adults. Perhaps most intriguingly, study of the bone microstructure revealed the animal was probably under a year old when it died. Together, all of these data showed that Parasaurolophus sprouted its crest at a smaller body size (and presumably younger age) than any of its known relatives, and grew its crest for a comparatively longer time. This developmental shift—described as heterochrony—explains in part the bizarre skull anatomy of the animal.

image

Silhouettes of adult and baby Parasaurolophus, relative to adult and baby humans. Credit: Copyright Scott Hartman (baby dinosaur), Matt Martyniuk (adult dinosaur), Andrew Farke (humans).

image

Reconstruction of the skeleton of a baby Parasaurolophus.Credit: Copyright Scott Hartman. Usage restrictions: This image is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

.

The whole package added up to something of broad scientific appeal—a baby dinosaur, scarcely a year old when it died, that offers groundbreaking new information on how an iconic prehistoric herbivore grew up. We were faced with the choice that many scientists face. Should we write a short paper—essentially an extended abstract a few pages long—and aim for a “high impact” journal, followed by a longer paper a few months or years or decades later? Based on past experience, this could mean months of shopping the manuscript around, with potentially little payoff in the end. And even if it did get published in that form, the paper would contain only a fraction of the information that other paleontologists wanted to know. Our research hit a topic of hot interest—growth changes in dinosaurs—and I felt a more complete paper would better serve the scientific community, as soon as possible.

So, as lead researcher on the study, I made a big decision. We were going to write the research up once, and we were going to write the most comprehensive, authoritative work possible. The work was a monster tome—46 pages single-spaced, with 11 tables and 28 figures. It covered virtually every aspect of the specimen, from skin to skull to microanatomy of the bones, along with extensive comparisons and interpretation. With this degree of detail, I knew that “conventional” academic publications could take months or years of review, editing and production (along with added charges for color figures). I also knew that I wanted the paper to be open access—every paleontologist, casual dinosaur fan, and even the proud parents, teachers, and classmates of my student co-authors should be able to access the paper with minimal hassle.

PeerJ emerged as the obvious home for our research. I was greatly impressed by the scientific quality of the papers previously published there, as well as the high production standards evidenced in attractive PDFs and a highly functional website. Plus, being a proponent of open access and a volunteer editor for the journal, I wanted to submit my best work to the journal. I wasn’t disappointed. The manuscript submission process was pretty painless, and the editor and reviewers who handled the manuscript gave it a thorough and fair critique. Scarcely 48 hours after submission of the revised manuscript, it was accepted and on the way to publication. The journal staff handling the paper have been responsive and professional—an excellent experience from start to finish.

image

Farke (top) and co-authors Annisa Herrero, Derek Chok, and Brandon Scolieri press the button to submit their manuscript to PeerJ. Credit: Andrew A. Farke.

Publishing in an open access journal like PeerJ is only one part of getting a fossil specimen out there. Those who make the trek to Claremont, California, can see the fossil on exhibit at the Raymond M. Alf Museum of Paleontology. But, not everyone has the ability to make such a journey. So, we’ve made this fossil the most digitally accessible dinosaur skeleton to date. All of the 3D digital data for the specimen are freely available, through supplementary information published with the article at PeerJ, data archives posted at Figshare, and high-resolution images on MorphoBank. Anyone who has an internet connection and the appropriate software can view the fossil from all angles, exploring the skeleton, plumbing the depths of the animal’s brain, and even testing our interpretations of internal anatomy. We’ve also set up a digital exhibit on the specimen, at www.dinosaurjoe.com. This fossil is part of our world’s biological heritage—and now the world can see it!”

 Dr. Andy Farke

A TEXT POST

Interview With an Author - Emma Schachner

Today’s Interview with an Author is with Dr. Emma Schachner, the corresponding author on "Pulmonary anatomy in the Nile crocodile and the evolution of unidirectional airflow in Archosauria", an article which has attracted quite a bit of interest in the paleontology community, culminating most recently with a spirited discussion in the comments thread of this article (discussing the benefits of the Open Peer Review that the article highlighted).  Dr. Schachner is a Postodoctoral Research Fellow at the University of Utah, in the Farmer Lab  (which, incidentally, has a particularly beautiful lab website!).

image


PJ: How did you first hear about PeerJ, and what were your initial impressions (i.e. before you submitted)?


ES: I had not heard of PeerJ before the journal was suggested as a possible place to submit our manuscript. I was wary at first because it is brand new, but once I heard that we could publish our reviews online I became very excited.

PJ: What persuaded you to submit to us?

ES: The idea to submit to PeerJ was suggested by one of my coauthors, John Hutchinson, who is also a PeerJ editor.

PJ: With this research, why did you choose to publish in PeerJ rather than some over venue?

ES: Once I was made aware of the transparent peer review process, along with the fact that the journal is both open access and very inexpensive to publish in, I was completely sold. Also our manuscript has a lot of colorful images, which can get very expensive in other journals.

PJ: What was your experience of the review process?

ES: The review process was fantastic. It was transparent and fast. The open review system allowed for direct communication between the authors and reviewers, generating a more refined final manuscript. I think that having open reviews is a great first step towards fixing the peer review system.

PJ: And what was your experience of the production process?

ES: The production process was very smooth and efficient. I was surprised by how quickly our manuscript flew through all the steps leading up to publication. There were no complicated figure uploads for large files, painful figure caption edits or anything like that. I appreciated the direct contact with a staff member of PeerJ versus a complicated digital interface.

PJ: What did you think to the overall speed of the process?

ES: As a postdoc, my experience with other journals is not as extensive as a senior researcher; however PeerJ was by far the fastest journal that I have interacted with. Particularly in the post-processing of the manuscript.
 
PJ: What did you think of the appearance of the PDF of the published article?

I very much like the blue color scheme. It helps to visually break up the paper into sections and make the figure captions stand out more. Personally I prefer the double columns because long and narrow figures can fit in nicely side by side with the text. The single column layout leaves a lot of unused space in the document.

PJ: And what do you think to the HTML view of your article?

ES: I love the HTML view. The ‘metrics data’ are a great way to monitor the status of your paper across multiple social networks. I like being able to track the number of page views. The rich hyperlinking is probably the best aspect of the HTML view. This feature alone makes the paper more accessible to other researchers than the traditional print article.

PJ: Was there anything that surprised you with your overall experience?

ES: Yes, three things: 1) that we were able to publish our reviews and our rebuttals online; 2) that we could submit the references in any format; and 3) I was able to directly email my final high resolution figures to the PeerJ staff instead of spending hours of my time uploading them and editing the captions.

PJ: Did any of your colleagues express anything to you about your publication with PeerJ?

ES: Yes. A few of my colleagues were concerned that because the journal was new, it might not be the best place for a young researcher to publish.

PJ: Now that you have been through the process, what is the advantage for an author to publish their work a) Open Access and b) with PeerJ

ES: a) Open Access is great. I really hope that science continues in this direction. It would be better for everyone, as more people will have access to publications, and academic institutions will not have to pay the exorbitant fees for access to the journal. b) PeerJ is unique in its transparent review process and published manuscript history. I absolutely love this.

PJ: Would you submit again, and would you recommend that your colleagues submit?

ES: Definitely, and I already have recommended PeerJ to my colleagues.

PJ: Many thanks for your time!

If you like what you hear about PeerJ, then try us for yourself. PeerJ is now open for your submissions at https://PeerJ.com and we are also now accepting preprints at https://PeerJ.com/preprints