Redrawing Ratite Relationships

A group of international scientists partly sequenced the genome of two extinct birds: the moa (New Zealand) and the elephant bird (Madagascar). Evolutionary analyses of their DNA reveal some surprising relationships.

Try to channel your inner David Attenborough voice for a moment and imagine him creeping through the shrubbery somewhere in Madagascar: ‘‘this is an elephant bird. Unable to fly, she is, if not the tallest, almost certainly the heaviest bird that ever lived on Earth, weighing nearly half a ton. And she is about to lay an equally impressive ten-kilogram egg.’’ Sadly, this is but a poor fictional rendering of an encounter that never happened.

What a way to start a scientific paper! Compare this with the usual dull opening sentences in other evolutionary studies, such  ‘Incongruence between phylogenies generated by different sets of genetic and phenotypic data poses a significant challenge in evolutionary biology‘ or ‘Hybridization, the interbreeding of species, has always intrigued ornithologists.‘ Are you still paying attention after these sentences? (Actually, these two lines are the opening sentences of two of my own papers…).

The paragraph quoted above was written by Florian Maderspacher (Senior Reviews Editor at the scientific journal Current Biology). His article is a kind of commentary on another paper published in Current Biology. In this study, Takahiro Yonezawa and colleagues unraveled the evolutionary history of the ratites, a group of flightless birds that contain among others, ostrich, emu, rhea and kiwi.

The exciting feature of this work is the sequencing of two extinct ratites: the moa and the elephant bird. The researchers obtained DNA from fossil bones and compared the DNA of these two giants with their living relatives. This led to some surprising findings…

First, the moas appear to be closely related to tinamous, a family of cryptic birds that hide in the understory for the South-American rainforest. Second, the giant elephant birds (which could reach up to three meters) are the closest cousins of the small, round, furry kiwis.

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The family tree of the ratites. (From Maderspacher, 2017)

As often (well, all the time) happens in science, new insights lead to new questions. The position of the tinamous within the ratites, for example, raises an intriguing dilemma. All the ratites are flightless, while the tinamous do fly. Did tinamous re-evolve their ability to fly? Or did flightlessness evolve separately in the different members of the ratite radiation?

And what happened with the elephant birds and the kiwis. They are closely related but occur on islands (Madagascar and New Zealand) that lie thousands of kilometers apart and have never been close to each other in Earth’s history. So, how the hell did these birds end up on their respective islands?!

Food for thought. Mmm, kiwis…

kiwi

References

Maderspacher F (2017). Evolution: Flight of the Ratites. Current biology : CB, 27 (3) PMID: 28171755

Yonezawa T, Segawa T, Mori H, Campos PF, Hongoh Y, Endo H, Akiyoshi A, Kohno N, Nishida S, Wu J, Jin H, Adachi J, Kishino H, Kurokawa K, Nogi Y, Tanabe H, Mukoyama H, Yoshida K, Rasoamiaramanana A, Yamagishi S, Hayashi Y, Yoshida A, Koike H, Akishinonomiya F, Willerslev E, & Hasegawa M (2017). Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites. Current biology : CB, 27 (1), 68-77 PMID: 27989673

The paper by Maderspacher also links to a clip by David Attenborough on moas. Enjoy!

Presentation Pitfalls: The Star Wars Syndrome

Today I was almost blinded during a presentation. Not by the remarkable beauty of the presenter or some elegant experimental design. No, I nearly lost my eyesight because the laser pointer was directed straight at my precious pupils.

Firstly, I don’t like the use of laser pointers during presentations. The (usually) red dot can be quite distracting while leading the audience through a cluttered powerpoint slide. I prefer to let the slides speak for themselves. The audience will find its way.

Also, the red dot can be a great indicator of the presenter’s stress levels. Trying to point at a figure with shaking and sweaty hands can result in an uncontrollably jumping red speck. Cats would love it. If you would still like to use a laser pointer while being at the verge of a nervous breakdown, just use your other hand to stabilize the hand holding the pointer.

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The presenter of today’s presentation was not nervous at all. He spoke fluently and explained his results nicely. He did, however, suffer from another laser pointer problem, namely the Star Wars Syndrome. After pointing at a figure or keyword on his slides, he forgot to let go of the button controlling the laser. As he continued talking and enthusiastically waved his arms, a small red dot bounced around the walls and ceiling. And occasionally threatened the eyesight of unsuspecting audience members. Again, cats would love it.

The solution to the Star Wars Syndrome is quite straightforward. Let go of the damn button! You don’t see Obi-Wan Kenobi, Luke Skywalker or Darth Vader swinging their lightsabers around willy-nilly. They use it wisely. Presenters should do the same with their laser pointers. Please take this advice to heart and may the Force be with you!

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Pearls and Perspectives

In 1870, the French writer Jules Verne published a science-fiction novel, entitled ‘ Twenty Thousand Leagues Under the Seas.’ The French professor Pierre Arronax, his Belgian servant Conseil, and the harpooner Ned Land end up on the Nautilus, a submarine controlled by the peculiar Captain Nemo. During one of their many adventures, they walk around the island of Ceylon (now known as Sri Lanka) in sophisticated diving equipment, looking for pearls. Before they explore the underwater world, professor Arronax explains what a pearl is:

To the poet, a pearl is a tear of the sea; to the Orientals, it is a drop of a dew solidified; to the ladies, it is a jewel of oblong shape, of a brilliancy of the mother-of-pearl substance, which they wear on their fingers, their necks, or their ears; for the chemist, it is a mixture of phosphate and carbonate of lime, with a little gelatine; and lastly, for naturalists, it is simply a morbid secretion of the organ that produces the mother-of-pearl amongst certain bivalves.

If you struggle through these long sentences, it becomes clear that a pearl can be many things, depending on your perspective. To romantic poets, it is ‘a tear of the sea’ , while for (wealthy) ladies it is precious jewel. Professor Arronax then turns to the scientific perspectives: chemistry and biology. The chemist focuses on the different chemical compounds, such as phosphate and carbonate. The naturalist, finally, is realistic and sees the pearl for what it is: the ‘morbid secretion’ of an enclosed mollusk. The paragraph ends here, but we could go even a step further. To the physicist, a pearl is a collection of atoms, each composed of neutrons, protons and electrons, which are in their turn composed of different quark flavors.

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A physicists’ perspective of a bird

These different views on a simple pearl highlight one of the most exciting characteristics of science: perspective. Give an object to a molecular biologist, a chemist, a physicist or an ecologist; and they will all tell you a different story.

I used to be a chemistry teacher. If you would have given me a pearl at that time, I would have told you about its chemical composition (as already explained by professor Arronax). Now, some years later, as a PhD in evolutionary biology, I would tell you about the evolutionary history of the creatures that make these jewels.

So, over these years, my perspective has changed. Ask me again in ten years and I may tell you another story (maybe as a nostalgic and romantic poet, describing the beauty of these molluscan miracles).

Here is another important lesson: perspectives change over time. You learn, you discover, you discuss, you think, and you change your mind. Or at least, in a perfect world, new information should trigger you to change your mind (if necessary). But often people adhere to their specific world view and ignore or reject new facts. Some might even refer to ‘alternative facts’ that better fit their world view (I could start writing about the new president of the USA, but I refuse to use that trump card here). By adhering so strongly to your view of the world, you restrict yourself and impede personal growth. So, open you mind! But, as fantasy author Terry Pratchett wrote, ‘The trouble with having an open mind, of course, is that people will insist on coming along and trying to put things in it.’ That is why we have to remain critical as well.

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The cover of ‘Twenty Thousand Leagues under the Sea’ by Jules Verne

From a paragraph in a 1870 science fiction book to an important life lesson (have an open mind, but remain critical). Just by changing our perspective and letting the waves of our minds carry us along. To end, some appropriate lyrics from the Pearl Jam (what did you expect?) song Tremor Christ:

Little secrets, tremors turned to quackes
The smallest oceans still get big, big waves

Dr. Jente Ottenburghs!

After more than four years of hard work, I finally obtained my PhD. On December 8th 2016 at 11.00 am, I successfully defended my thesis, entitled Crossing species Boundaries: the Hybrid Histories of the True Geese. The thesis committee rated my thesis as ‘very good’ and my defense as ‘excellent’. After that day, I escaped to the UK for a well-deserved holiday (although I assisted my girlfriend in some lab work). Now, back on the European mainland, I am ready to reflect on one of the most memorable days in my life.

 

The layman’s talk

I arrived in the Aula of Wageningen University around 10.00 am to prepare for my defense. After setting up the Powerpoint presentation for my layman’s talk and getting into my fancy suit, the first guests arrived: my family. My parents stayed in a local B&B (my former room) and walked to the Aula, while my sister and her boyfriend transported my two grandmothers from Belgium. They all entered together, some of them more nervous than me.

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The family arrives at the Aula

While the other guests were arriving, I retreated to the ‘small auditorium’ where I was joined by my two paranymphs: Shenglai Yin and Yingying Wang (my two Chinese office mates). The presence of paranymphs is a tradition at certain Dutch universities. Wikipedia has the following to say about this custom:

In the Netherlands, paranymphs (paranimfen) can be present at the doctoral thesis defence. This ritual originates from the ancient concept where obtaining a doctorate was seen as a de facto marriage to the university. Furthermore the paranymphs would also act as a backup for the doctoral candidate to ask for advice when answering questions. Today their role is symbolic and seen as a position of honour similar to a best man or woman at a wedding.

A couple of minutes before the start of the defense, the ‘pedel’ entered the room to explain the ceremony to us. Then, just before the clock hit 11.00 am, she guided us to the Aula.

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The pedel explaining the ceremony to me (on the right) and my paranymphs

Once the audience settled down, I started my layman’s talk. The idea of this presentation is to present your PhD thesis (more than four years of work!) in about 14 minutes. Everyone should be able to understand it. I based this talk on my experiences at ScienceBattle, a Dutch theater show in which four PhD students try to convince the audience about their research. I managed to win this event a couple of times (being rewarded with a wooden plaque of the ScienceBattle logo and a brain in a jar. What more can you wish for?), so I was quite confident that laymen would be able to understand it.

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The layman’s talk

 

The Defense

After the layman’s talk, the thesis committee entered, preceded by the pedel. They took their seats and prof. dr. Carolien Kroeze, representing the rector magnificus, opened the ceremony with a firm bang of her hammer. Then it was time for the opponents to attack my work and fire question after question on me. I cannot remember all the questions, but let me give you a brief overview.

Prof. dr. Bas Zwaan, professor of genetics at Wageningen University, was the first to challenge me. He mainly focused on several concepts in the study of speciation, such as genomic islands and Dobzhansky-Muller incompatibilities, and how they relate to the geese.

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Prof. dr. Bas Zwaan (Wageningen University)

Second, dr. Pim Arntzen (senior researcher at Naturalis Biodiversity Center) took the floor. Among other things, he asked me about the evidence for a hybrid origin of the Red-breasted Goose. And he wanted me to elaborate on one of my propositions, namely ‘Coffee breaks lead to more important insights than conferences and workshops.’

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dr. Pim Arntzen (Naturalis Biodiversity Center, Leiden)

The next one in line was prof. dr. Bart Nolet from the Netherlands Institute of Ecology. He mainly focused on the behavioral mechanisms leading to hybridization. He also gave me a figure of the distribution of Canada Goose subspecies with the question: what is going on here? Subspecies in the north are smaller, probably because of natural selection for shorter extremeties (a phenomenon known as Allen’s Rule).

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prof. dr. Bart Nolet (Netherlands Institute of Ecology, Wageningen)

Another member of the Netherlands Institute of Ecology, dr. Kees van Oers, was given the opportunity to question me. This opponent deserves a special mention. Originally, the fourth member of my examining committee was dr. Radka Reifova from the university of Prague. Unfortunately, she could not make it to Wageningen. Because she cancelled just one week before my defense, we had to rush to find another opponent. Only one day before the defense dr. Kees van Oers agreed to fill in. Thank you very much, highly esteemed opponent! Much to my delight, he started with a philosophical question: ‘What is a species?’ We had a lively discussion on this topic.

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dr. Kees van Oers (Netherlands Institute of Ecology)

My co-promotor, dr. Hendrik-Jan Megens, concluded the interrogation with some questions related to my upcoming postdoc in Uppsala. After 45 minutes, the pedel entered again and hit the ground with her stick. ‘Hora est!’ The committee withdrew for consultation and I just had to wait and see.

About 15 minutes later, the committee returned. I was invited to sign my degree. A very memorable moment (and a mandatory picture moment). Afterwards, my promotor, Ron Ydenberg, delivered the judicium and the laudatio. The verdict from the committee: my thesis was ‘very good’ and my defense was ‘excellent.’ With a big smile on my face and the degree in my hands, I walked out of the Aula.

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Signing my degree

Following the defense, all the guests had the opportunity to congratulate me and enjoy a lunch at the reception. After shaking many hands and receiving several presents, I finally made my way to the table with sandwiches, only to find out that the selection had been narrowed down to ‘krentenbollen’.

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Group picture of my thesis committee and supervising team at the reception. 

 

The Party

In the evening, I invited my family and friends to H41, a cosy restaurant in downtown Wageningen. After several beers, it was time for speeches. Shenglai Yin opened the floor with a nice stand-up comedy routine. Then Sip van Wieren, Herbert Prins and Hendrik-Jan Megens took the microphone. I will not repeat their speeches here, but to summarize: Sip elaborated on our plans to work on goose penises, Herbert described my encounter with a Russian lady in Siberia, and Hendrik-Jan talked about my stubborn character.

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Sip ending his speech
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Herbert doing what his does best: talking
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Hendrik-Jan giving his speech

In the end, I got back at all my supervisors and thanked them with a special present: six decoy geese (the ones hunters use to lure geese).

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My supervising team and their geese

The party continued. Finally, everyone went home, including me. The next day, I woke up quite early. Staring at the ceiling, I realized that I was now a doctor. Although I did not feel different. I was still (and will be) just Jente.

Thank you all for sharing this memorable day with me. And a special thanks to Audrie for taking pictures.

Evolutionary Comedy!

The evidence for evolution is overwhelming. Many books have been written, including Why Evolution is True by Jerry Coyne and The Greatest Show on Earth by Richard Dawkins. Despite the general acceptance of evolution by the scientific community, creationists continue to “attack” evolutionary theory. These attacks provide valuable material for comedians. Here is one of my favorite comedians, the Irish Dara O’Briain, on the evidence for evolution:

And the following clip on science is my all time favorite. Enjoy!

My First Citation, Due To A Couple Of Hybridizing Scaups

Thursday, the 3rd of December. Salekhard, Russia. After a busy conference day filled with talks on waterfowl, I am checking my e-mails in the Yuribei hotel. Suddenly, my attention is drawn by a message from Research Gate: “Jente, you have a new citation.” There it is, my first citation!

 

H-index

Although it is definitely not equivalent to publishing your first paper, the first citation can be seen as  milestone in an early scientific career.  A citation indicates that people are reading your work, which is often the result of a significant amount of blood, sweat and tears. Moreover, the fact that your paper is cited, shows that your work is considered relevant by other scientists. I have to admit: seeing my Ibis paper cited in another paper, brings forth to a satisfactory feeling of accomplishment. Indeed, that night I fell asleep with an ear-to-ear smile.

This citation also means that from now on, I am the proud owner of an H-index (i.e. a scholar with an index of h has published h papers each of which has been cited in other papers at least h times).  In my case, I have an H-index of 1, because one paper has been cited one time. A humble index, but it is a start…

 

'She didn't want to go out with you even though you told her you had a h-index of 37! Boy I don't understand women!'

 

Scaups

But what about the paper that cited me? Well, it was written by Philip Lavretsky (Wright State University) et al. and deals with hybridization between Lesser Scaup (Aythya affinis) and Greater Scaup (A. marila). Apart from geese (my study species), Scaups are now some of my favorite bird species!

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One of my new favorite birds: the Greater Scaup (picture by Teddy Llovet)

 

 

References

Lavretsky, P., Peters, J., Winker, K., Bahn, V., Kulikova, I., Zhuravlev, Y., Wilson, R., Barger, C., Gurney, K., & Mccracken, K. (2015). Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations Molecular Ecology DOI: 10.1111/mec.13487

Projects, papers and other pleasures

It has been a while since I wrote something on this blog (June 8 to be precise). And this has a reason: I have been extremely busy working on my PhD. So, as an update, I will give a short overview of my accomplishments and future plans.

todolist fish

The Avian Hybrids Project

First of all, I published the first paper of my PhD! In the ornithological journal Ibis, I announce the website Avian Hybrids, on which I have gathered the bulk of scientific literature on avian hybridization. Keeping this website up to date did cost me a lot of time, but it also attracted quite some publicity. Recently, the British Ornithological Union (BOU) asked me to write about the Avian Hybrids Project on their blog. My story appeared online earlier this week.

Here are the links:

My paper: http://onlinelibrary.wiley.com/doi/10.1111/ibi.12285/full

The Avian Hybrids website: https://avianhybrids.wordpress.com/

The BOU blog: http://www.bou.org.uk/avian-hybrids-project/

Papers

Apart from the Avian Hybrids Project, I have been working on a number of papers. Two have been submitted. If they get accepted and published, I will discuss them on this blog! In the meanwhile, I am working on the next set of papers. The first results look promising…

Finally, I also have a girlfriend since a couple of months. I guess she deserves some of my time as well…

peer review

(Self-)References
Ottenburghs, J., Ydenberg, R., Van Hooft, P., Van Wieren, S., & Prins, H. (2015). The Avian Hybrids Project: gathering the scientific literature on avian hybridization Ibis, 157 (4), 892-894 DOI: 10.1111/ibi.12285