What does a bird curator do? Part II

As a component of the professional training in FLIGHTLOSS, I have the unique opportunity to learn from the best through a bespoke curatorial program. Thus, I will spend at least a day with each curator to do hands-on work in the collections, which will provide me with experience that is hard to get by. After spending a day with Hein and a Magpie, next up were the anatomical collections with Senior Curator Joanne Cooper and Curator Judith White.

Among the alcohol specimens, I did some inventory and strategic reshuffling, marvelling at the some really cool specimens. I even nailed the species ID for an unidentified specimen. Pickles can be stored rather differently depending on size and abundance…

For skeleton specimens, the bulk of the prep work is actually outcourced—to beetles. Once they have munched away, there is still some more cleaning to do. After that follows the task to permanently label each and every bone with the voucher (registration) number of the specimen. A task that requires patience and precision! Finally, since I am working on flight loss in birds, I must throw in a photo of a flightless celebrity!

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What does a bird curator do? Part I

My project FLIGHTLOSS aims to uncover the genomic architecture of convergent loss of flight in rails. But there’s more to research than the research, and there are more career paths than being a university professor. I have the benefit of carrying out my project at the Natural History Museum, which houses one of the (two) largest bird collections in the world (the other one being the American Museum of Natural History). The bird collection is at NHM’s branch in Tring, northwest of London, and comprises a mind-blowing >1,000,000 specimens! I am a member of the Bird Group, which—you guessed it—cares for the ornithological collections. It currently consists of six permanent curatorial staff; all with their own specialty. Because what is in the collection? Stuffed birds, right? Nope, it’s quite a lot more diverse than that. The majority of the specimens in collection, about a quarter million, are indeed skins (“stuffed birds”). But there are also 20,000 skeletons, 20,000 spirit specimens (“pickles”), 300,000 egg clutches, and 4,000 nests!

A Magpie’s gotta get clean somehow.

As a component of the professional training in FLIGHTLOSS, I have the unique opportunity to learn from the best through a bespoke curatorial program. Thus, I will spend at least a day with each curator to do hands-on work in the collections, which will provide me with experience that is hard to get by. First out was spending a day with Senior Curator Hein van Grouw, mainly in the prep lab. While the additions to the skin collection is considerably less extensive compared to historical times, there are still new birds to process. Thus, my friend for the day was a Magpie that had met a sudden death, and spent quite some time in a freezer. Skin prep really is a craft, and it takes many tens (or actually probably hundreds) of birds to become good at it. I have previously had the opportunity to learn the basics with Collections Manager Chris Wood, at the University of Washington Burke Museum, so I’ll throw in a non-Magpie photo of some of my previous achievements too!

All done, only drying left (for a long time) before registration.

Some of my preps from the Burke Museum. Fancier pin work, fancier pins. (Fancier birds?)

Getting historical in Stockholm

Historical? Me? No, actually not. But I’ve spent a lovely (though insanely intense*) time at the Swedish Museum of Natural History, working with historic DNA.

Most bird specimens in museum collections are prepared as study skins, i.e. they look like birds lying flat on their back. In order to obtain a tissue sample for DNA extraction, while causing minimal damage to the specimen, the most common method is to cut thin scrapes of dermal tissue from a toepad. For my EU-funded FLIGHTLOSS project, I have obtained such samples from several rail species, and additionally I have processed other samples for some exciting side projects.

Under the guidance of Dr. Martin Irestedt, I have learnt to implement the local flavor of best practices and protocols for work with toepad samples. In short, in a clean lab (protected from the contamination of DNA from any modern source) I have extracted DNA. Unlike from fresh tissue, the DNA in historic specimens is degraded and broken up in small fragments. I have sorted out fragments of an appropriate length and turned them into libraries, which will be sequenced on an Illumina Novaseq, which spits out millions and millions of sequence reads. These can then be stitched together against the reference genome of a closely related species.

All in all, the visit was very successful, and I managed to create sequencing libraries from 48 out of 49 samples. Working with historical samples, there’s always a bit of randomness included, and usually one would expect more than one sample out of fifty to fail, so I am stoked! I am extra happy and proud to have successfully extracted DNA from an extinct parakeet, which was collected in the 1770 on one of Captain Cook’s journeys.

*The bulk of my samples were sent by courier from the UK and should have arrived before me. Instead, the courier screwed up, and I spent days waiting for the samples to arrive. But I couldn’t just reschedule my trip back, so let’s just say I din’t see much more than the lab in Stockholm.

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.

New digs

It will be a while before any results come out of the FLIGHTLOSS project, because obtaining sample loans from all over the world in the middle of a pandemic is not exactly an easy particularly fast process. Meanwhile, what does your work set-up look like? Don’t you have a Barn Owl supporting your laptop?

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 in the FLIGHTLOSS project, 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).