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…

Goose Demography.jpg

 

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.

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Dr. Jente Ottenburghs

This post has been taken from my other blog: Evolutionary Stories

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.

New Review-paper in Frontiers in Zoology

A couple of months ago, I walked into the office of my supervisor with a brilliant idea (according to me, at least…). I had been working on the General Introduction of my dissertation and realized that one section could be upgraded into a separate chapter, and perhaps even a publication. Luckily, my supervisor agreed and I started writing a review on hybridization in geese.

And that review was recently published in Frontiers in Zoology, an open-access journal:  http://frontiersinzoology.biomedcentral.com/articles/10.1186/s12983-016-0153-1

Abstract:

The high incidence of hybridization in waterfowl (ducks, geese and swans) makes this bird group an excellent study system to answer questions related to the evolution and maintenance of species boundaries. However, knowledge on waterfowl hybridization is biased towards ducks, with a large knowledge gap in geese. In this review, we assemble the available information on hybrid geese by focusing on three main themes: (1) incidence and frequency, (2) behavioural mechanisms leading to hybridization, and (3) hybrid fertility. Hybridization in geese is common on a species-level, but rare on a per-individual level. An overview of the different behavioural mechanisms indicates that forced extra-pair copulations and interspecific nest parasisitm can both lead to hybridization. Other sources of hybrids include hybridization in captivity and vagrant geese, which may both lead to a scarcity of conspecifics. The different mechanisms are not mutually exclusive and it is currently not possible to discriminate between the different 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. The knowledge on hybrid geese should be used, in combination with the information available on hybridization in ducks, to study the process of avian speciation.

Avian Genomics in San Diego

In the beginning of January, I traveled to to San Diego, California (my first time in the USA!) to give a talk at the annual Plant and Genomics Conference, better known as PAG. My colleague Robert Kraus organized a session on Avian Genomics and invited me to present my work on hybridization in geese (you can find the PDF of the presentation here).  Here is the exciting program of the session:

  • Generating a Bird Genome Resource: Insights into the Avian Tree of Life, Complex Traits and Genome Evolution (Erich Jarvis, Duke University Medical Center)
  • Non-model Avian Genomics Fit for Purpose – the End of the Model Organism? (David W. Burt, Roslin Institute, University of Edinburgh)
  • Comparative Population Genomics of Birds (Robb T. Brumfield, Louisiana State University)
  • The Challenges of Repetitive DNA in Avian Comparative Genomic (Alexander Suh, Department of Evolutionary Biology, Uppsala University)
  • The Role of Hybridization in the Evolutionary History of Geese (Jente Ottenburghs, Resource Ecology Group, Wageningen University)
  • Genomics and Speciation: The New World Mallard Complex (Philip Lavretsky, University of Miami-Florida)

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Success of the Month!

Recently, I was awarded the “Success of the Month” at my department (Environmental Sciences Group) for three reasons:

  1. My talk at the waterfowl conference in Salekhard (Russia)
  2. My participation in the theater show ScienceBattle
  3. My publication (and accompanying website) in Ibis

Below you can read the (Dutch) announcement for my award.

Succes van de Maand voor Jente Ottenburghs

De directie heeft het Succes van de Maand toegekend aan Jente Ottenburghs, promovendus bij de leerstoelgroep Resource Ecology. De belangrijkste reden voor deze toekenning is de wijze waarop Jente over zijn werk communiceert. Niet alleen met publicaties en op symposia, maar ook in het theater.

Ganzen zijn trouwe partners, behalve als ze vreemd gaan. Soms kruisen ze zelfs met andere soorten. Jente Ottenburghs onderzoekt wat er gebeurt als er kruisingen ontstaan en genetisch materiaal schijnbaar willekeurig binnen en tussen soorten wordt verspreid. Dit kan bijvoorbeeld gevolgen hebben voor het aanpassingsvermogen van de dieren. Hierover hield Jente een lezing in Salekhard (Siberië) tijdens het 4-jaarlijkse congres van jagers en jachtonderzoekers uit de Russische Federatie, China, Scandinavië en Nederland. Jente’s onderzoek over hybridisatie tussen ganzen maakte daar zo’n indruk dat een motie werd aangenomen, waarin Finse onderzoekers ervoor pleitten dat er speciaal met zijn inzichten rekening zou moeten worden gehouden voor opvattingen omtrent duurzame jacht.

Jente treedt niet alleen op bij symposia, maar ook in het theater. Hij doet met enige regelmaat mee aan de ScienceBattle, een theaterwedstrijd waarbij jonge promovendi in 10 minuten aan een algemeen publiek moeten uitleggen wat ze doen. Het publiek jureert de bijdragen. “Hij doet dat geweldig, als een echte stand-up comedian, en hij heeft in zowel Boxmeer als Wageningen (Junushof) zo’n wedstrijd gewonnen,” zegt zijn promotor Herbert Prins.

 

Ook heeft Jente een nieuwe vorm van publiceren geïntroduceerd in het ornithologische toptijdschrift IBIS. Gekoppeld aan dat tijdschrift is nu een link naar een website van hem, waarbij hij citizen science gebruikt om informatie over vogelhybriden op een wetenschappelijk verantwoorde wijze te verzamelen en rubriceren. Die informatie gebruikt hij vervolgens om door middel van zijn diepgaand genetisch werk te onderzoeken hoe het soortsconcept, bij watervogels en in het bijzonder ganzen, gemoderniseerd kan worden .

Herbert Prins: “Jente experimenteert dus heel succesvol met nieuwe vormen van wetenschap waarbij het publiek wordt betrokken, en zijn fundamentele wetenschap wordt direct opgenomen in de praktijk, zelfs in zo’n ‘cultureel resistente omgeving’ als de Russische Federatie. Ik heb daar grote bewondering voor.

My ScienceBattle victory in Boxmeer