Fishy birds, birdy fish, poisonous fungi, and pizza: Our “scientific breakthroughs” published in predatory journal


Did you see Dan Baldassarre’s wonderful paper entitled “What’s the Deal with Birds?” published on April 1 (!) last year? If not, you’re in for a treat. Dan did something that I had been thinking of for quite a while, namely to reply to one of the countless requests for manuscripts that he, I, and probably most scientists who have ever published anything, receive from predatory journals. He decided to write up some crap, submit it, and try to get it published, to prove a point. You can retroactively follow the whole saga in his Twitter thread, and very well-deserved, the story received quite a bit of attention. And what’s not to like? Dan concluded that birds are weird, and a partial result was that penguins look like fish (weird).

Figure 1 from Baldassarre (2020).

Well, like I said, I had been planning on doing something similar for quite a while and discussed it with my friend Danny Haelewaters. Since I am an ornithologist who, at the time, worked on fish, and since Danny is a mycologist, we thought that Dan Baldassarre’s initial explorations were noteworthy, but felt that they could be expanded and go deeper. Thus, we embarked on a truly interdisciplinary collaboration that made use of cutting-edge methodology, and we could expand Dan Baldassarres’s observation quite dramatically:

As the attentive reader will have seen, we can draw several conclusions from our study. As a side result, it turns out that barn swallows and flying fish are sister lineages (quite the taxonomic earthquake!). For the main result, we predict that penguins will re-evolve flight as poisonous fungi colonize the Antarctic, if the temperature rises, and this decreased fishiness will increase the chances of you ordering a penguin pizza in the future! Didn’t quite catch that? Well, read our ground-breaking paper, and as a bonus you might pick one or two hints at the publishing industry (and other things)!

Writing this paper was fun and quick, and it has been accepted for publication in multiple journals. However, we were less successful than Dan Baldassarre at haggling to get it published without paying the ridiculous publication fees that makes up the core of the business model for predatory journals. So, it has taken until now to finally get this paper published, but along the way, we have received some golden nuggets, such as this “peer review report” from the Journal of Ecosystems and Ecography:

Our paper is now out in the Oceanography & Fisheries Open Access Journal, published by predatory Juniper Publishers. So what—and why? I am sure that some of you will think this is just rubbish, and that’s fine. Some might even find it NOT funny, or perhaps even vulgar. Well, I think that our paper very clearly demonstrates the total lack of review and the sole interest of profiting on authors that the predatory journal industry rests upon.* We further intend to deal with this in a more formal and serious manner, using our fishy bird paper as an example. Keep your eyes open for that!

Reference: Stervander M & Haelewaters D. 2020. Fishiness of piscine birds linked to absence of poisonous fungi but not pizza. Oceanography & Fisheries Open Access Journal 12(5): 555850. DOI: 10.19080/OFOAJ.2020.12.555850.

 

Update 1: We do not regret the least that our reference no. 4 is no longer available on its original platform.

Update 2: *Does this work? What have other attempts looked like? Zen Faulkes have collected and curated “sting papers” such as ours in an online volume, Stinging the Predators—A collection of papers that should never have been published. This collection comprises 340 pages worth of sting papers and analysis. We are, of course, happy that our paper has been included as no. 33 in version 17 of this freely available resource!

Update 3: Sam Perrin has written a blog post at Ecology for the Masses, where he broke down our paper “for the benefit of those outside the scientific community who may not understand complex jargon like ‘pizza toppingness’ and ‘random selection by dart'”. We’re talking serious #SciComm here! Also (as can be seen in the comments below), Jerry Coyne has written a blog post about our paper, commenting more generally on hoax/sting papers and predatory journals.

Publication bonanza!


Last week saw a bizarre coincidental release of multiple publications in which I and many co-authors have put in lots of work during the past few months to the past few years.

The paper on the evolutionary history of the Galápagos Rail, mentioned in my previous post, was published and is available as Open Access at the journal website. Lead author for this super fun collaboration was Jaime Chaves.

I had the great privilege of formally describing a taxon new to science, a new subspecies of Red-capped Lark Calandrella cinerea rufipecta ssp. nov. that is restricted to the Jos Plateau in Nigeria. In the paper, we discuss taxonomy of the genus, and species delimitation across the whole lark family. The paper is available as Open Access at the journal website.

I have also been involved in the Bird10K project, which released its first publication of the second phase, in which the full genomes of representatives of almost all bird families have been sequenced. This work, which is a huge collaboration spearheaded by Shaohong Feng and Josefin Stiller, was published in Nature, where it is available as Open Access.

For full information about the papers, see my page on peer-reviewed research. Also, check in my book chapters section, as a long-awaited showpiece of a book came hot off the presses. It is the book The Largest Avian Radiation – The Evolution of Perching Birds, or the Order Passeriformes, edited by Jon Fjeldså, Per GP Ericson, and Les Christidis. Jon has also painted a huge number of beautiful illustrations, which on their own make this book a must on the coffee table. I have contributed a large-scale time-calibrated backbone phylogeny of all passerines. The book is for sale at Lynx Edicions.

Rails, rails, and rails at the Natural History Muesum

I started my Marie Skłodowska-Curie fellowship at the Natural History Museum in London/Tring three days ago, and have been busy with paperwork, introductions, meeting lovely new people, and being awestruck but the magnificent buildings, history, and collections. Here, I will spend the coming couple of years investigating the genomic underpinnings of the convergent evolution of flight loss in island rails.

Today, I had the privilege of looking at one of these rails that have not quite lost its flight ability yet, but is somewhere along the trajectory: a Galápagos Rail Laterallus spilonota collected by Charles Darwin himself. The timing could not have been better, as this was the same day that a new preprint came out on bioRxiv about the evolutionary history of the Galápagos Rail!

I have been lucky enough to join a collaboration headed by Jaime Chaves at SFSU, where I helped assemble mitochondrial genomes from century-old specimens from the California Academy of Sciences, and then used those for phylogenetic analyses. We confirm that the Galápagos Rail is the sister of the Black Rail L. jamaicensis on mainland North and South America, and that it colonized the Galápagos Islands about 1.2 million years ago. Sanger sequencing three genetic loci in modern samples shows that present-day populations on different islands display low genetic diversity, and somewhat surprisingly are not differentiated, indicating ongoing gene flow. So perhaps the Galápagos Rails still use their wings after all!

Part of Figure 1a from Chaves et al. (2020) shows a dated phylogeny based on mitochondrial genomes. Here, the Galápagos Rail Laterallus spilonota comes out as a sister to the Inaccessible Island Rail L. (formerly Atlantisia) rogersi, simply because the no mitochondrial genomes have been sequenced for the two other species in the clade—Black Rail L. jamaicensis and Dot-winged Crake L. (formerly Porzana) spiloptera. The illustrations in the figure from Chaves et al. (2020) is reproduced with permission from Lynx Edicions ©.

This is a great way to start on the collaboration with Jaime, who will continue to be involved in my FLIGHTLOSS project.

Read more about the Galápagos Rails at bioRxiv.

Songbird Showpiece of Passerine Power

I am very happy that the huge efforts into a book on the passerine radiation, that I was fortunate to take some part in, are nearing fruition.

Led by Jon Fjeldså, with co-editors Les Cristidis and Per GP Ericson, this monster book (estimated at 3 kg!) should adorn the book shelf or coffee table of any ornithologist or birder who cares about passerines. And who doesn’t? With >6,000 species, passerines make up 60% if avian diversity, and is a remarkable order that rapidly diversified and spread across all continents but Antarctica. They comprise a crazy diversity of plumage, vocalization, behavior, and ecology!

If you learned your birds some 10–20 years ago or earlier, you will know that lots of (annoying?) rearrangements and reclassifications have happened lately. This is because traditional taxonomy often sorted birds into large, ecologically-based groups, like warblers or finches, since the morphological differences were relatively small. Over the past couple of decades, DNA-based studies have revealed time and time again that these relationships were not what we thought. Here, we try to set the record straight, and propose a new classification and linear taxonomy based on the evolutionary history of passerines.

My contributions to the book is the back-bone phylogeny and chronology, represented in one chapter and one appendix. There are also many other thematic chapters, as well as a whole section going through all the passerine families. The book is illustrated with hundreds and hundreds of watercolor paintings by Jon Fjeldså, a reason on its own to get the book!

If you are interested, read more and perhaps place a discounted pre-order with Lynx Edicions by June 30th! The book is expected to come hot off the printers in mid-July. Enjoy!

Citation: Fjeldså J, Christidis L & Ericson PGP (eds). The largest avian radiation – the evolution of perching birds, or the order Passeriformes. Under production, Lynx Edicions (Barcelona). [My specific contributions are listed here.]

Flightless rails at the NHMUK

I am delighted to say that next step on my academic journey will take me to the Natural History Museum in London/Tring, UK, for a two-year project with the somewhat pompous title The genomic underpinnings of convergent evolution: Repeated loss of flight in island rails, the greatest avian colonizers. Starting this fall, I will be hosted by Alex Bond, Senior Curator in Charge of the amazing bird collections, and I will collaborate closely with Jaime Chaves at SFSU.

This project is made possible by the European Union, who has awarded me a Marie Skłodowska Curie fellowship.

Photo of the flightless Inaccessible Island Rail: Martim Melo (c). Photo of NHM London by Diliff, licensed under CC BY-SA 3.0 at http://tiny.cc/o8zojz.

Ornis Svecica fledges again

When I joined the editorial board of BirdLife Sweden‘s peer-reviewed ornithological journal Ornis Svecica in 2017, I had quite a few ideas of things that I thought could be improved. The journal has been published since 1991, and caters to academic researchers as well as non-professional ornithologists. It is a great resource with no publishing or article processing fees, but very little had changed since the founding of the journal. Late last year, the publisher made the decision to stop printing the journal, which forced a kick-start overhaul in order to find a new solution for the journal, where all material could be easily accessible online. I was glad to be appointed Managing Editor, and since then I have worked hard together with Editor-in-Chief Sören Svensson and the rest of the editorial board to achieve this goal. I am therefore pleased to say that Ornis Svecica relaunches as an open access, no fees, online only journal on the World Migratory Bird Day, May 11, 2019. Check out the site at http://os.birdlife.se, learn something about the foraging prerequisites of Ortolan Buntings or the range expansion of European Stonechats and see what you think of the new graphic profile, and read some more of my thoughts in this editorial. Any new articles will be published shortly after acceptance in a continuous publication model. I hope you will enjoy – and I hope you’ll consider submitting a contribution!

The cover of Ornis Svecica’s relaunch Volume 29 features a beautiful photo of an Ortolan Bunting by Ivan Sjögren (c).

How did the world’s smallest flightless bird end up on Inaccessible Island?

We recently published a paper in Molecular Phylogenetics and Evolution on the origin and taxonomy of the Inaccessible Island Rail Atlantisia rogersi. The paper is available, with free access to anyone, until December 7, via this link. I summarized our findings in a Twitter thread, that I will share here. Photos, where nothing else is stated: Peter G. Ryan.

Continue reading

How can we make fieldwork less dangerous?

In June, I participated in the excellent workshop for Evolutionary Quantitative Genetics, generously supported by the Society for the Study of Evolution (SSE). During a lecture Brian O’Meara mentioned Richard Conniff’s the Wall of the Dead, or the Memorial of Fallen Naturalists, and I just couldn’t let go of it. Reading the entries at the Wall of the Dead, I started wondering if certain fields of study were over-represented. It turned out that Talia Yuki Moore was also wondering things, and would like to draw conclusions from the tragic incidents in order to prevent future field work casualties.

We thus joined efforts, and contacted Richard Conniff about analyzing the material to better understand the circumstances and causes of scientist mortality during fieldwork. However, Conniff’s Wall of the Dead certainly is not exhaustive, and we are now therefore making a call for more information. Do you know of someone who is missing from this list? If so, please add their information to our database. Your contribution will help establish new safety standards for fieldwork and memorialize the contributions of those who gave their lives to further our understanding of the natural world.

Please contribute your information to our form, where you can also read more about the study, which is an IRB exempt study registered with the University of Michigan Institutional Review Board (#HUM00149801). We will forward all new entries to Richard Conniff’s Wall of the Dead. We will also account for all entries in upcoming publications, whether they will be included in our analyses or not (depending on whether they match certain criteria).

Also, please forward this call for information widely. If you have any questions, do not hesitate to contact me or Talia (taliaym /at umich.edu).

Me and Peter Ryan fighting our way through heavy mist and strong winds, during field work on Inaccessible Island in 2011. Photo (video still) (c) Martim Melo.

Me and Peter Ryan fighting our way through heavy mist and strong winds, during field work on Inaccessible Island in 2011. Photo (video still): (c) Martim Melo.

I, an Oregonian fish researcher

How did this happen to a bird researcher from Sweden? Well, evolutionary questions can be addressed in various study systems, and I will make use of the crazy syngnathid fish (seahorses, pipefish, and seadragons) to look into craniofacial development and evolution. I am happy to do this in the Cresko Lab at the Institute of Ecology and Evolution, University of Oregon. I started my three-year postdoc project in August 2017.

Cresko Lab sticklebacks showing development of lateral plates. Figure from Cresko (2008) Science: https://doi.org/10.1126/science.1165663.

[This post has been back-dated to reflect reality…]