A Personal Report of the Hybrid Symposium in Hamburg (June 12-14)

Recently, I attended a conference about hybridization in Hamburg (Germany). When I saw the line-up of speakers (among others James Mallet, Nick Barton and Simon Martin), I registered right away. And my high expectations were certainly met. Here is a personal overview of three days of hybrid science!

 

DAY 1

What the F*ck are Species?

The symposium started on Tuesday 12th of June with a plenary talk by James Mallet. He has been studying hybridization between mimicry races of Heliconius butterflies for some time and provided a nice overview of this work. Recent genomic analyses of these South American butterflies resulted in a surprising conclusion: only 2 percent of the genome follows the species tree whereas the remaining 98 percent is flowing freely. This result complicates the question of what species actually are. No wonder James’ Twitter-account is called @WTF_R_species

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A collection of Heliconius butterflies.

 

DAY 2

Hybrid Flowers

The second day of the symposium opened with another familiar name in the hybrid community: Nick Barton. He has produced some classical papers on hybridization and hybrid zones, such as “Analysis of Hybrid Zones” and “The Role of Hybridization in Evolution.” A large part of his work focuses on the theoretical analyses of hybrid zones (read: a lot of mathematics). When I heard him asking for some chalks, I prepared myself for a bombartment of mathematical formulas on the blackboard. However, he mainly talked about recent work on the Antirrhinum flowers hybrid zone where they found several islands of divergence in the genome, which were formed by a combination of gene flow and multiple selective sweeps. Read more about this work here.

The next talk also focused on flowers. Mario Vallejo-Marin explained how hybridization and whole genome duplication work together to shape the evolution of monkeyflowers (genus Mimulus). Interestingly, whole genome duplication can save fertility in hybrids that are normally sterile.

The final speaker of the morning session, Kenneth Whitney, presented the latest results of an experimental approach to hybridization research. His group assessed the fitness of sunflower hybrids (genus Helianthus). Field experiments showed that hybrids evolve faster and have increased fitness compared to “pure” species. This suggests that hybridization can speed up adaptation. However, genetic analyses indicated that the hybrids have acquired genetic material from local plants, which might explain why they adapted so quickly. Kenneth thinks that hybrids are more likely to pick up genes from other plants because they have less self-incompatibility alleles. But this hypothesis remains to be tested. You can read more about these finding here.

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The three types of flowers from this session: Antirrhinum (left), Mimilus (topright) and Helianthus (bottomright).

 

Fish, Snails and Ants

After the coffee break, Arne Nolte kicked off with the evolution of sex determination in Cottus fish. In contrast to mammals and birds, these fish do not have separate sex chromosomes. It turns out that in hybrids, sex is largely determined by dominant alleles at multiple loci that act side by side. About 10% is driven by additive effects at other loci.

The next talk, by Ingo Schlupp, also revolved around fish, namely the Amazon Molly. This peculiar species is of hybrid origin and reproduces clonally. However, in order to reproduce the females need sperm, which they obtain from other species. This system is known as gynogenesis.

Anja Marie Westram stayed closed to the water and presented her work on Littorina snails. These animals come in two ecotypes, a “wave” form that is adapted to life on the rocky shores where waves come crashing in and a “crab” form that resides between the rocks where it hides from predators (i.e. crabs). These ecotypes interbreed along hybrid zones. Anja Marie compared several of these hybrid zones and found mainly concordant patterns. A nice example of replicating hybrid zones.

The final talk before lunch required extra attention, because Jurgen Gadau introduced us into the wonderful world of harvester ants. When these ants mate with the same genetic lineage, they produce queens. But when they mate with a different lineage, you get workers. Jurgen is trying to figure out how such a system evolved and can be maintained.

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Red harvester ants

 

Molecular Plant Biology

Because I am not really a plant person, the next session was more challenging for me: three talks on the molecular mechanisms in plant hybrids. Definitely interesting but not always easy to follow. First, Luca Comai talked about chromosome remodelling. Apparently, some hybrids eleminate half of their genome, partioning it into micronuclei. Some of these fragments curl up into ring chromosomes (as already described by Barbara McClintock) and could potentially transfer genes between species. Second, Paul Grini introduced the AGAMOUS-like (AGL) transcription factors. Some of these genes are misexpressed in Arabidopsis hybrids, resulting in dead seeds. Detailed analyses showed that things go wrong during the endosperm cellularization. Finally, I learned a bit more about how plants can become polyploid (i.e. having more than two pairs of chromosomes). The goup of Arp Schnittger has figured out that this is due to  problems at the Spindle Assembly Checkpoint (SAC) during cell division. The cell tries to separate the chromosomes but eventually gives up and continues, resulting in polyploidy.

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The model system plant: Arabidopsis thaliana.

 

Some More Plants

After a long and exciting poster session, we re-assembled for the final two talks of the day. Jeffrey Chen kicked off with stories about the hybrid origin of cotton and the balance between stress and growth in Arabidopsis hybrids. There are too many details to cover here, so I will redirect you to the original publications in Genome Biology and Nature Communications.

The final talk of the day was given by Richard Abbott. He explained how climate change can lead to more hybridization events as species expand into new areas. He gave examples of secondary contact between willow trees and possible adaptive introgression in Chinese cypresses. Climate change can also lead to habitat disturbance which could facilitate hybridization (as already pointed out by Edgar Anderson in the 1940s). It turns out that the UK and Ireland are the perfect places to test this idea. Many hybrids have managed to establish themselves here, as exemplified by the book Hybrid Flora of the British Isles. Richard told us the fascinating story of Senecio plants in the UK. It turned out that one species (S. squalidus) was actually a hybrid that originated in Italy on the slopes of mount Etna. Who knew?

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A hybrid plant species: Senecio squalidus.

 

DAY 3

Butterflies and Beetles

The third day began later than planned because Zacharia Gompert could not make it. The first talk of the day was by Simon Martin who introduced us to a peculiar study system in Africa: the butterfly Danaus chrysippus. These butterflies come in several mimicry morphs that are determined by three loci. They hybridize in a contact zone in eastern Africa where some weird things are going on. First, males are killed by the endosymbiont Spiroplasma, leading a biased sex ratio with mostly females. Second, some individuals have evolved a new sex-chromosome by fusing two other ones. Simon is trying to figure out how these three processes – hybridization, male killing and neo-sex-chromosome – interact with each other. Exciting work.

The next talk also revolved around insects and their bacteria. The work of Susanne Dobbler deals with beetles that have been infected with three different strains of Wolbachia. The outcome is the same as with the butterflies: no males are produced by infected females. However, the uninfected females also mostly produce females. The exact reason behind this pattern remains elusive but it might have something to do with mito-nuclear incompatibilities.

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A colorful specimen of Danaus chrysippus.

 

From Plants to Yeast

The next session was an all-female line-up, prompting the chair (Stefan Hoth) to wonder if some male killing occurred. The session was started by Eunyoung Chae who explained how deleterious interactions between particular immune receptors (NLRs) in hybrid plants result in an auto-immine response in plants, culminating in hybrid necrosis.

Kirsten Bomblies introduced another species of Arabidopsis, namely A. arenosa, which occurs in diploid and autotetraploid lineages. Kirsten managed to retrace the gene flow patterns between several populations. For example, genes flowed from the western Carpatians through the Baltic into a railway site in Berchtesgaden, helping the latter adapt to local conditions. A nice example of adaptive introgression.

The next speaker, Wei Yuan, switched back to everyone’s favorite model system: Arabidopsis thaliana. She analyses transcriptomic data in hybrids and uncovered a set of more than 1000 non-additively expressed genes that can be divided over five functional modules. She is now planning to disentangle the patterns within and between these modules.

Susanne Edelmann presented similar work for Brassica napus. But instead of working with transcriptomic data, she focused on methylation patterns (which correlate with gene expression levels). She found less methylation in hybrids which could explain higher growth rates.

The final speaker, Rike Stelkens, turned away from plants and presented her work on experimental evolution in yeast. Her lab crosses two species (Saccharomyces cerevisiae and S paradoxus) that are 14 percent divergence. That is ten times as divergent as humans and chimps. Several experiments show that the hybrids do better than their parental species, probably because of particular recombination patterns. You can find more information about this work in this pre-print.

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A closer look at Saccharomyces cerevisiae

 

Patterns of Introgression

The final session of the symposium was kicked off by Gerard Heckel who studies the radiation of Microtus voles. These small rodents are infected with the Tula-virus and there seems to be co-divergence between the voles and the virus. Gerard nicely illustrated this process with a Russian doll cartoon: when the voles diverge, their pathogens (i.e. the Russian dolls inside) hitchhike along and also diverge. Next, Diethard Tautz presented a new method to quantify phylogenetic discordance. Applying this method to mouse and human data uncovered some interesting patterns of introgression.

Before the plenary talk by Rosemary Grant, the poster prizes were distributed. To my big surprise, I was awarded third place. I really enjoyed the poster session but I would not have expected to win something. And Rosemary’s talk? That was a wonderful story about her work (with her partner Peter Grant) on the Darwin’s Finches. I will not try to provide a short summary here. Just read their papers and books. I can definitely recommend The Beak of the Finch by Jonathan Weiner.

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The winners of the poster prizes (I am standing in the middle).

How to run a successful science blog

I have been running my blog Avian Hybrids for a couple of years now. This blog has grown over the years, attracting a loyal readership and getting some attention from scientists and bloggers. In my humble opinion, it has become a successful science blog. Or to rephrase it, I am happy with the current status of the blog. In this blog post, I would like to share my ideas and experiences on how to run a successful science blog (i.e. a blog that makes you feel satisfied).

 

1. Don’t do it for the clicks

There are many (science) blogs out there. The competition for ‘clicks’ is fierce. If you want to create a blog to attract visitors, you can start writing about food, fashion or celebrities. To me, this feels like selling your soul to the devil. It is okay to write mindless posts about your favorite pasta dish, but will you feel satisfied with this?

I once wrote a blog post on how spoonbills manage to eat big frogs (they actually break their limbs one by one). I posted this article – with the catchy title “Break a Leg” – on Reddit. The result: more than 700 views in one day! But somehow I did not feel satisfied. Most readers just glanced over the article without really being interested. My goal is to teach people something new, not to support them in their procrastination.

clickbait

 

2. Find your niche

As I wrote above, there are many science blogs. There is a lot of information on the internet. If you want to stand out from the crowd, you will have to find your own niche. For example, there are so many blogs on evolution. My first blog – Evolutionary Stories – could not compete with the more established ones.

Luckily, I managed to find my audience with my blog on hybridization in birds. To my knowledge, I am the only person blogging about the scientific papers on avian hybrids. There is another blog – Bird Hybrids – that focuses on how to recognize certain hybrids, but we cover different topics and that blog is not so active (last post is from 8 May 2017).

'See, Baldwin? It's all about finding your niche.'

 

3. Content, content, content

If you want to establish your blog, you will need to create a lot of content. This will be very difficult in the beginning. You will write several blog posts, only to see that nobody is reading them. My advice here: keep writing. Eventually, people will find your blog and start reading it on a regular basis. Some of my earliest posts are still being read to this day. For example, my first blog post on Avian Hybrids (in 2014) – Thrush Migration and Speciation – has attracted four readers this year. Not much, but it’s better than nothing.

Another benefit from a lot of content is that you can refer to previous blog posts in your writing. I always to try to add links to related posts so interested readers can click and check out older stories. Make sure that a new window pops up when readers click on your link. You don’t want them to get lost while browsing through your blogging history.

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4. Sharing is caring

Just writing a lot of posts won’t attract a lot of readers. You will also need to actively advertise your blog. The best way to do this is through social media. Share your posts on Facebook, Twitter, Instagram, … Again, in the beginning, this might not attract many readers. But keep sharing!

In addition to social media, I also contact the authors of the papers I blog about. I have only received positive reactions when doing this. Scientists feel proud when their work is picked up by other people. They appreciate the effort and often send you other papers to blog about. Not only will you attract new readers, you are also expanding your network.

social media

 

5. Write positive

My final tip is more personal. During my years in the blogosphere, I have noticed that I prefer to add a positive vibe to my writing. It is easy to write critical posts about how someone else is wrong. For instance, I used to regularly write articles about the flawed arguments of creationists. They often misrepresent evolutionary biology and spread lies. But attacking creationists did not make me feel satisfied . The negative tone of the posts bothered me (and there were other issues, you can read about that here). So, I decided to focus on positive things, namely the latest findings in research on avian hybrids.

So…I wrote a fantasy book

I sat down behind my laptop and looked out the window. It was dark outside. “Just fifteen minutes,” I told myself. I started the timer on my cellphone and let my fingers brush over the keyboard. At first, the words came out slowly, but after a few minutes the sentences were almost magically appearing on my screen. I drifted off, totally immersed in the developing story. Suddenly, my writing flow was broken by an annoying beeping sound. My cellphone was vibrating. The fifteen minutes were over. I put my cellphone aside and continued typing. About an hour later, I closed my laptop. 

This short story describes one of my successful writing sessions. Getting into the zone and producing several paragraphs. Unfortunately, not every evening went this smoothly. There were times when I barely filled the fifteen minutes with writing. But if you want to write a book, you cannot wait for inspiration to strike. Flashes of real inspiration are rare. So, I forced myself to write for at least fifteen minutes every evening. It paid off. I finished my first fantasy novel a few months ago: The Dragon with the Blue Scale.

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The cover of my fantasy book.

 

Why?

Why did I want to write a book? It felt like to logical thing to do. A large part of my time involves writing. For my work –  as a postdoctoral researcher – I write technical papers on the evolution of birds. In my free time, I write blog posts about bird hybrids. And occasionally, I contribute to the Dutch popular science website Scientias.

I have always dreamed about writing a book. It seems like the ultimate goal for a writer. So, I didn’t think about it too much and just started writing. The main story for my book has been in my head for some years. It was just a matter of putting it on paper.

 

What?

What is the book about? It is difficult to describe because it contains several disparate elements. You could describe it as a detective story in a fantasy world with some elements from science fiction. Hopefully, the synopsis will bring some clarity.

On the planet Hodra, dragons and people live peacefully together. But the quiet society is shaken up by a series of kidnappings. Several children disappear without any trace of the culprit. Detective Charlie has almost given up until someone sees a dragon flying away with a child in its claws. The dragon is pitch black with a striking blue scale. The intense search of Charlie – assisted by the clumsy trainee Freddie – suddenly becomes even more difficult, when a civil war breaks out on Hodra and General Oana commits a military coup.

What follows is an action-packed adventure in which several characters travel across Hodra – and even to other planets – to solve this mystery.

 

And now?

The book will be published this year (in April or May) by Beefcake Publishing. This publisher works with crowdfunding: the more money we collect, the more books will be published. The crowdfunding is also reward-based, meaning that you get something in return. For a contribution of 20 euros, for example, you will get a copy of my book. If you donate 50 euros, you get two extra books from the publisher.

The only issue for my international friends is that the book is written in Dutch. Perhaps there will be an English version some day. I can imagine you don’t want to buy a book you cannot read, but perhaps you have some Dutch friends or you just want to support my book project. All support is welcome.

Here is the link to the crowdfunding:

https://crowdfunding.beefcakepublishing.be/product/de-draak-met-de-blauwe-schub/

 

New publication! A review paper on hybrid speciation in birds

Last week, I published my first single-author paper in a peer-reviewed journal. In the paper, entitled “Exploring the hybrid speciation continuum in birds”, I review the evidence for several hybrid bird species and propose a new way of classifying hybrid species. Here is the abstract.

Hybridization is increasingly recognized as a creative evolutionary force contributing to adaptation and speciation. Homoploid hybrid speciation—the process in which hybridization results in a stable, fertile, and reproductively isolated hybrid lineage where there is no change in ploidy—has been documented in several taxa. Hybridization can directly contribute to reproductive isolation or reinforce it at a later stage. Alternatively, hybridization might not be related to the evolution of reproductive isolation. To account for these different scenarios, I propose to discriminate between two types of hybrid speciation: type I where reproductive isolation is a direct consequence of hybridization and type II where it is the by‐product of other processes. I illustrate the applicability of this classification scheme with avian examples. To my knowledge, seven hybrid bird species have been proposed: Italian sparrow, Audubon’s warbler, Genovesa mockingbird, Hawaiian duck, red‐breasted goose, golden‐crowned manakin, and a recent lineage of Darwin’s finches on the island of Daphne Major (“Big Bird”). All studies provide convincing evidence for hybridization, but do not always confidently discriminate between scenarios of hybrid speciation and recurrent introgressive hybridization. The build‐up of reproductive isolation between the hybrid species and their parental taxa is mainly driven by premating isolation mechanisms and comparable to classical speciation events. One hybrid species can be classified as type I (“Big Bird”) while three species constitute type II hybrid species (Italian sparrow, Audubon’s warbler, and golden‐crowned manakin). The diversity in hybrid bird species across a range of divergence times also provides an excellent opportunity to study the evolution of hybrid genomes in terms of genome stabilization and adaptation.

 

Link to the paper: https://onlinelibrary.wiley.com/doi/10.1002/ece3.4558

My blog post about it: https://avianhybrids.wordpress.com/2018/12/07/how-many-hybrid-bird-species-are-there/

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Red-breasted goose, a hybrid species?

 

How to be a prolific writer? Try the Asimov Approach

September started. The summer break is over. Soon my weekly schedule will be filled with lab meetings, journal clubs and seminars. During July and August I have taken advantage of my empty agenda to focus on writing. Here is a quick overview of the output: 25 blog posts for the Avian Hybrids Project, 5 pieces for the Dutch popular science website Scientias and two submitted manuscripts (one has been accepted, the other is currently in review). And I finished another creative writing project on the side. Not a bad summer…

 

Asimov – A Prolific Writer

I managed to produce so much content by following the writing approach of Isaac Asimov. This American author and professor of biochemistry is the textbook example of a prolific writer. He wrote and edited more than 500 books, and he published in nine of the ten major categories of the Dewey Decimal Classification. Science fiction fans probably know him for the Foundation series and the Robot series. An impressive body of work.

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Isaac Asimov – a prolific writer

 

A Foundation for Productive Writing

How did Asimov manage to write so much? Here are three reasons:

  1. Write every day, also if you don’t feel like it. Asimov believed there was no such thing as writer’s block. His father had a candy store in Brooklyn and opened his doors at 6 am every day. And he never complained about ‘shop keeper’s block.’
  2. Use a simple (but clear) writing style. When Writer’s Digest asked Asimov the secret to his prolific writing, he replied, “I guess I’m prolific because I have a simple and straightforward style.”
  3. Don’t care about your critics. You can keep editing your text, but at some point you will have to publish it (or submit it to a journal). There will always be people to comment on your work. Don’t think about the criticism too much and just get it out there.

These three writing tips have definitely contributed to my summer output. This does, however, not mean that they will work for you. But do give them a try, you never know…

Embracing Diversity – Academia and the Refugee Crisis

In my home country Belgium – like the rest of Europe – there is currently a big debate on giving shelter to refugees. The biggest political party in Belgium, the NVA, is advocating a policy to close the borders and evict illegal immigrants. Refugees are not seen as human beings. They are supposedly threatening ‘Belgian culture.’

However, in the entire discourse nobody has ever defined ‘Belgian culture.’ Are these refugees going to take away our fries and Belgian waffles? Or are they planning to overthrow our Christian values (although the majority of Belgians – understandably – does not attend church services any more)? In my mind, Belgian culture is a social construct. You happen to be born within the artificial borders of one of the smallest countries in the world.

Politicians are creating an unrealistic straw man of refugees: uneducated criminals that come here to take over our culture and steal our jobs. Every society has criminals. Some refugees might have a criminal record, but the same holds true for many Belgians. But does this mean that you have to close the borders for all refugees?

Working in academia exposes you to many different cultures. Over the years, I have worked with people from numerous countries (see the list below) and from different religions and ideologies. When talking with someone, we would always find some common interest. It makes you realize that they are all interesting people regardless of where they come from. I urge the politicians to talk with refugees and see them for what they really are: fellow human beings.

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My current research group with people from Belgium, Latvia, United States, Sweden, Poland, Austria, China and Iran.

 

The List of Nationalities

  • Australia
  • Austria
  • Belgium
  • Bolivia
  • Brazil
  • Canada
  • Chile
  • China
  • Colombia
  • Costa Rica
  • Czech Republic
  • Denmark
  • Ecuador
  • Egypt
  • Ethopia
  • Finland
  • France
  • Germany
  • Ghana
  • Guatemala
  • Hungary
  • India
  • Indonesia
  • Iran
  • Israel
  • Italy
  • Japan
  • Kenya
  • Latvia
  • Mexico
  • Nepal
  • Netherlands
  • Norway
  • Panama
  • Peru
  • Poland
  • Portugal
  • Russia
  • South Africa
  • South Korea
  • Spain
  • Sweden
  • Switzerland
  • Tanzania
  • Turkey
  • United States
  • Uruguay

 

Why I Write…

Many scientists do not like writing. They enjoy doing fieldwork or fiddling around in the lab, but they dreadfully await the day when they have to start writing. I actually enjoy writing. And I try to do it as often as possible (whether it is for my blogs or for a paper). Here are the main reasons why I write.

I just enjoy writing. Plain and simple.

Writing helps me to understand often complex concepts. By writing it out for other people, I am also teaching myself about the subject. In some respect, I am applying the Feynman Technique.

Sharing knowledge with the general public is an important part of being a scientist. However, most scientists rely on journalists to inform the public. Although there are many good science journalists out there, they can make mistakes. You are the expert in your field, so write about it.

Writing also helps me build a scientific network. I often share my blogposts with the authors of the paper I wrote about (by mail or Twitter). It’s a nice way to introduce yourself to the scientific community and get into touch with “the big names”. For example, when I started my new job in Uppsala, someone asked me: “Are you the guy behind the website about bird hybrids?”

The scientific publishing process is glacially slow. It takes some time to write the paper, taking into the account the comments and wishes of your co-authors. Once submitted to a journal, it can take several months before it gets accepted (if it gets accepted). I don’t have the patience to wait for this. That is why I like to write blogposts or short article for the Dutch website Scientias. You write and it quickly appears online. Instant gratification!

By writing a lot, I also improve my writing (at least, I hope so). So, here I can give you some very simple and straightforward advice: if you want to improve your writing, just write…

Why do you write? Or why do you hate writing? Feel free to share your experiences in the comments section below.

writing

How I (try to) get things done

What is the best way to achieve your goals? There are numerous books, websites and Youtube videos dedicated to this question, but in the end it is something personal. My advice would be to try out different things and see what works for you. Over the years, that is exactly what I did. Here is a brief insight into my strategy.

 

1. Don’t try to remember things

How often does is happen that something pops up in your head: “I should water the plants” or “I need to respond to that e-mail.” The moment those thoughts fly by, you decide to remember to do it later. And what happens: you forget…

To avoid this from happening, I follow the advice of Daniel J. Levitin in his book The Organized Mindwrite it down! Our minds are constantly being bombarded with information. So, we need to keep our mind clear. To get rid of all the excess information, I use the software Wunderlist. Every time something comes to my mind, I write it down in this app (which I have on my phone and my computer).

I actually used this strategy before, but I kept forgetting to look at the list of things to do. And I could not add “look at the list” to my to-do-list, because well… Therefore, I have made Wunderlist the homepage on my internet browser. The first things that pops up is my to do list!

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Wunderlist: a great app to keep a to do list.

 

2. Keep track of your progress

When you are doing research, you are constantly juggling several projects at a time. In my case, I am currently dividing my time over these subjects:

  • Finishing my project at the Karolinska Institutet
  • Starting a new project at Uppsala University
  • Managing my blog Avian Hybrids
  • Popular Science writing (mostly for Scientias)

You can image that it can be difficult to keep track of all these different projects. To have an overview, I use the app Trello, which allows you to make ‘boards’ for different projects. The nice thing is that you can subdivide tasks within each project into sizable chunks so you don’t get overwhelmed by the work ahead of you. Below is a screenshot of Trello.

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Trello: keep track of your projects.

 

3. Have a plan for the day

Did you ever arrive at work not knowing what to do, although you have mountain of work waiting for you? So, you start checking Facebook and Twitter instead. To avoid procrastinating (also see number 4), make sure you have a plan for the day. Ideally, you write it down the day before.

I use the two apps mentioned above (Wunderlist and Trello) to get an idea of what needs to be done. Which tasks are urgent? Or quick? Do I have a deadline for a certain project? Based on urgency, priority and time, I make a plan for the day. And then: just do it!

If you need some extra motivation, just watch this video…

 

4. Avoid distractions

When things get difficult or boring, your mind tends to wander off. Before you know it, you are surfing the internet. Scrolling through Facebook. Watching cat videos. Or reading random news websites. It also happened to me. Unconsciously, I would open my browser and start exploring the internet. To avoid this from happening, I use a website blocker, preventing me visiting certain websites. Very effective!

 

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I hope these tips are useful. But remember, some of these things might not work for you. Just give it a try and find your best strategy to get things done!

Scientific Publishing: Failure is also an option

Yesterday I recieved the confirmation that my manuscript for the Dutch journal Limosa will be sent to the editor for the final touch. Four years ago, I tried to publish a similar paper in the same journal, but it got rejected (and rightfully so!). Looking through my old mails, I discovered many more rejections. Most people only see the published papers and don’t know about the several rejections and revisions leading up to the final publication. So, I will give an overview of my rejected manuscripts during my PhD. My published papers are highlighted in bold:

  • Patterns of hybridization in geese (Wildfowl, 2013)
  • The generic concept in ornithology: Monophyly and introgressive hybridization as criteria (Ibis, 2013)
  • A generic classification of Anatidae (ducks, geese and swans) based on monophyly and introgressive hybridization (The Auk, 2013)
  • Hybrid geese in the Netherlands (Limosa, 2013)
  • Hybridization to distinguish between natural and anthropogenic hybridization between goose species (Ardea, 2013)
  • A generic classification of Anatidae (ducks, geese and swans) based on monophyly and introgressive hybridization (Journal of Ornithology, 2013)
  • Hybridization in birds: an update (Science, 2015)
  • The Avian Hybrids Project: gathering the scientific literature on avian hybridization (Ibis, 2015)
  • A Modern Synthesis of Avian Hybrids Zones and Patterns of Introgression (Biological Reviews, 2016)
  • Hybridization in Geese: A Review (Frontiers in Zoology, 2016)
  • A Tree of Geese: A Phylogenomic Perspective on the Evolutionary History of True Geese (Molecular Phylogenetics and Evolution, 2016)
  • A Modern Synthesis of Avian Hybrids Zones and Patterns of Introgression (BMC Biology, 2016)
  • Birds in a Bush: Towards an Avian Phylogenetic Network (The Auk, 2016)
  • A Modern Synthesis of Avian Hybrids Zones and Patterns of Introgression (Journal of Avian Biology, 2016)
  • A History of Hybrids: Genomic Patterns of Introgression in the True Geese (Evolution, 2016 – cascaded down to Ecology and Evolution)
  • A History of Hybrids? Genomic Patterns of Introgression in the True Geese (BMC Evolutionary Biology, 2017)
  • Avian Introgression in the Genomic Era (Avian Research, 2017)

 

As you can see, I suffered many rejections before publishing my first paper in Ibis. All my publishing attempts in 2013 – with a manuscript on the use of hybridization in taxonomy – can be seen as a wild goose chase. The idea was interesting but not feasible (I now realize). However, my fruitless attempts introduced me to the peer-review system of plublishing and helped me improve my scientific writing skills.

In 2016, I published several papers in quick succession. There was, however, one big manuscript that kept haunting me. A long review on avian hybrid zones and introgressive hybridization was rejected three times (Biological Reviews, BMC Biology and Journal of Avian Biology). The rejections were mainly due to the summarizing nature of this manuscript. The reviewers wanted to see more future directions. So, this year, I decided to shorten the paper and focus on the use of genomic tools. This manuscript – Avian Introgression in the Genomic Era – was published recently in Avian Research. A lesson in pragmatism.

This overview of failures nicely illustrates that scientific publishing is not easy, but that you can learn how to increase your chances of getting a paper accepted. As Winston Churchill said: “Success consists of going from failure to failure without loss of enthusiasm.”

 

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A Trilogy of Goose Papers

With the publication of ‘A History of Hybrids? Genomic Patterns of Introgression in the True Geese’ in BMC Evolutionary Biology, the three goose papers from my PhD thesis have made it into scientific journals. The trilogy is complete, but the story continues…

During my PhD, I studied the evolutionary history of the True Geese. This bird group contains about 17 species (depending on which authority you follow) and is traditionally divided into two genera: Anser and Branta. At the start of my PhD, I was surprised to find out that the phylogeny (i.e. evolutionary tree) of the geese was still unresolved. The failure to resolve the relationships between these bird species is probably due to high levels of hybridization. My goal was to solve this phylogenetic conundrum and further explore the influence of hybridization during the evolutionary history of the True Geese.

 

Part 1: Goose Hybrids

Although the main focus of my research was to quantify the effects of hybridization on an evolutionary timescale, I wanted to know the current state of events. How often do birders see hybrid geese? Which species are interbreeding? Are these hybrids fertile? And why does a goose choose a partner of another species? These questions formed the basis for part one of the goose trilogy. This first story was published in Frontiers in Zoology, entitled ‘Hybridization in Geese: A Review’.

It turns out that the majority of goose species have interbred at some point (in captivity or in the wild). Hybrids are thus common on a species-level, but rare on a per-individual level. The origin of particular goose hybrids is difficult to deduce but several mechanisms, such as interspecific nest parasitism and extra-pair copulations, are possible. The different mechanisms are not mutually exclusive and it is currently not possible to discriminate between these mechanisms without quantitative data.

Most hybrid geese are fertile; only in crosses between distantly related species do female hybrids become sterile. This fertility pattern, which is in line with Haldane’s Rule, may facilitate interspecific gene flow between closely related species. This finding is important for the other stories in the goose trilogy.

nest parasitism

 

Part 2: A Tree of Geese

Before I could investigate the role of hybridization in goose evolution, I needed a proper phylogenetic framework. The construction of this framework was the focus of my second story, which was published in Molecular Phylogenetics and Evolution under the title ‘A Tree of Geese: A Phylogenomic Perspective on the Evolutionary History of True Geese‘.

For this study, I collected blood samples from all goose species. Sequencing the whole genome of these species provided me with a huge amount of data to resolve the phylogenetic tree of this bird group. I won’t bother you with the technical details (e.g., we opted for an exon-based approach with both concatenation and consensus analyses). Let’s jump straight to the main results!

The split between Anser and Branta was already well-established, but the relationships within these genera were contentious. Using whole genome data, I was able to resolve the phylogenetic relationships between the different goose species.

Within the genus Branta (commonly referred to as the Black Geese) there is a group of White-cheeked Geese – Canada Goose (B. canadensis), Cackling Goose (B. hutchinsii), Barnacle Goose (B. leucopsis) and Hawaiian Goose (B. sandvicensis) – and two basal splits – leading to Brent Goose (B. bernicla) and Red-breasted Goose (B. ruficollis).

In the genus Anser, the most basal split leads to the morphologically divergent Bar-headed Goose (A. indicus). Next, two main groups can be recognised: the White Geese – Snow Goose (A. caerulescens), Ross’ Goose (A. rossii) and Emperor Goose (A. canagicus) – and the Grey Geese – Greylag Goose (A. anser), Swan Goose (A. cygnoides), the White-fronted Geese (A. albifrons and A. erythropus) and the Bean Goose complex (A. fabalis, A. serrirostris and A. brachyrhynchus).

A molecular clock analysis indicated that the majority of speciation events took place at the end of the Pliocene. The approximate date of diversification coincides with the beginning of a period of climatic oscillations between 3.2 and 1.9 million years ago. This period was part of a fast global cooling trend, following the closure of the Panama Seaway and the uplifting of the Tibetan Plateau around four million years ago. This resulted in the formation of permanent Northern Hemisphere ice sheets, the establishment of a circumpolar tundra belt and the emergence of temperate grasslands, which opened up new ecological niches in which new groups of animals and plants were able to spread. The tundra habitat serves as breeding ground for geese, while the temperate grasslands act as wintering grounds where mate choice takes place. Moreover, these tundra and grassland habitats provided ample opportunity for geese to explore new ecological niches and diversify in beak morphology.

A Tree of Geese

More importantly, the comparison of different gene trees revealed that different genes tell different stories. This observation, called gene tree discordance, can be caused by rapid speciation (leading to a phenomenon known as incomplete lineage sorting or ILS) and hybridization. Disentangling the contributions of ILS and hybridization is the focus of the third story.

 

Part 3: A History of Hybrids

And so we arrive at the final story in this trilogy where I explored the role of hybridization during the evolutionary history of the True Geese. As mentioned in the introduction, this story was published in BMC Evolutionary Biology, entitled ‘A History of Hybrids? Genomic Patterns of Introgression in the True Geese‘.

I found indications for ancient gene flow during the diversification of the True Geese and I was able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose.

The reconstruction of historical effective population sizes shows that most species experienced a steady increase during the Pliocene and Pleistocene (in agreement with the conclusions from story 2). These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow.

I can definitely conclude that the evolution of goose species follows a complex speciation model high levels of gene flow during species diversification. Unfortunately, I did not have the data to determine whether this gene flow is the outcome of (repeated) secondary contact or divergence-with-gene-flow. This warrants a population genomic approach whereby multiple individuals of one population are sequenced. In fact, this is exactly what I plan to do during my postdoc with Hans Ellegren at Uppsala University.

To be continued…

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Apart from the goose trilogy, I explored avian hybridization in general, culminating in two papers (and a third one on the way). These were published in the ornithological journals Ibis and The Auk.