When the speciation gene finds you

Building on decades of classical genetics research, we discovered that certain genes controlling vegetative compatibility in the fungus Podospora anserina act as speciation genes. But exactly how did we notice?

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Chances are, you’ve never heard of the fungus Podospora anserina, even though it’s considered a model organism in several areas of molecular biology. Indeed, “Podosporologists” are a rare breed, mostly endemic to France, Germany and the Netherlands. Or they were at least until 2015, when my PhD supervisor Dr. Hanna Johannesson got an ERC grant and decided to expand their range to Sweden. Hanna’s group had been working on meiotic drivers, selfish genetic elements that cause segregation distortion, in Neurospora species. Hanna knew from previous studies that P. anserina’s genome also harbors meiotic drivers, and she was interested in studying their evolution. So, Hanna contacted well-known Podosporologists and started a fruitful connection with Dr. Fons Debets and Dr. Eric Bastiaans in Wageningen University and Research, the Netherlands.

The Podospora team from Uppsala, Bordeaux and Wageningen
The Podospora team from Uppsala, Bordeaux, and Wageningen

Eventually, Eric came to Uppsala as a postdoc and brought along a precious collection of P. anserina strains that had been sampled in Wageningen since the early 90s. It was Eric who trained me to work with Podospora during the first year of my PhD and who did the work to get the whole Wageningen population sequenced. As Eric was leaving back to Wageningen, Dr. Aaron Vogan joined as a postdoc too. Together, Aaron and I took the challenge of solving the decades-long puzzle of meiotic drive genetics in P. anserina… but very quickly it became obvious we needed help. We needed somebody with molecular biology skills in Podospora. Thus, Hanna contacted Dr. Sven Saupe and his group, including Dr. Corinne Clavé and M.Sc. Alexandra Granger-Farbos, from Bordeaux University, France.

Sven agreed to visit Uppsala so we could present our data and plans. At the end of the meeting, Sven noticed that amongst our collection we had sequenced the genome of a particular strain called Y. It turns out, Corinne and Alexandra had been working hard to study a special locus known as het-v, and that the strain Y had a specific het-v allele that they hadn’t been able to sequence. Sven asked me to extract the sequence of that locus from the Y genome and send it to them, and so I did.

Months later I had finally obtained a set of single nucleotide polymorphisms (SNPs) from the Wageningen collection. We were interested in finding evidence of population structure connected somehow to the multiple meiotic drivers. Instead, I found basically no variation at all. The Wageningen strains were nearly identical. Of course, I was very disappointed. As a first exploratory analysis, I made a phylogenetic tree with the SNP data. And lo and behold, there was a very strongly supported branch dividing the population in half. This is fungi we are talking about, it is not rare to find cryptic species in sympatry. But upon closer inspection, I saw this branch was mostly coming from a single region in chromosome 5 and hence felt like it was an artifact of an analysis with largely uninformative data. However, Aaron got inspired by my tree and in a moment of genius decided to recode mating success data hidden in a Wageningen PhD thesis from 20051. He analyzed the data as a distance matrix… and ran directly to my office.

- “The clusters of mating data match your phylogeny perfectly!!”

The project became suddenly very exciting. We needed to know exactly what was in that chromosome 5 region. I opened the genome browser IGV in my computer, and nervously scrolled all the way to the region. I gasped.

 - “Aaron, I know what that is. I know exactly what this sequence is… it’s het-v”.

"I know what that is... it's het-v!

It was precisely the same locus I had sent to the Bordeaux team. We realized that we could distinguished two reproductively isolated groups just by looking at their het-v allele. But we were very confused. How could het-v, a gene involved in vegetative fusion between fungal individuals (aka. allorecognition), be related to reproductive incompatibility? This might not be obvious for a non-mycologist, but it would be equivalent as saying that genes controlling tissue compatibility during organ transplants has something to do with speciation. Oh wait, that is exactly what some people have suggested for the major histocompatibility complex (MHC) locus in jawed vertebrates2!

We contacted Sven right away. He told us that het-v made perfect sense, in fact. Already from the 60s and 70s, the classic geneticists Jean Bernet and Jacques Labarère had figured out that het-v interacts with another locus, het-r, and that their interaction had pleiotropic effects on sexual compatibility! The Bordeaux team had spent years finding and characterizing het-r 3, and now they were trying to get at het-v. But they had been interested in the allorecognition part. Now, we were all interested in the sexual part.

From that point onward, the project shifted drastically. The het-v project in Bordeaux fused with ours. We knew that het genes typically evolve under balancing selection, and analyses of our population data supported that expectation. I went back into Wageningen in 2016 and 2017, and sampled a lot more strains with the help of M.Sc. Suzette de Groot. The results confirmed that the reproductively isolated groups defined by het-v co-exist in time and space. Clearly, balancing selection could definitely be at play here. But we needed to understand exactly how het-v and het-r were splitting the population. Finally, Dr. Ivain Martinossi-Allibert joined the team as a postdoc and used individual-based simulations to clarify the dynamics of the system. The conclusion: allorecognition genes that were pleiotropic on sexual recognition can induce reproductive isolation while evolving under balancing selection and some degree of non-random mating like selfing or inbreeding. Unlike the MHC case, sympatry is needed for balancing selection to operate and maintain the reproductively isolated groups.

In the end, we did solve the miotic drive puzzle4,5, but clearly het-v and het-r also have a major role to play in the evolution of this fungus, and likely its relatives too. Hanna often said that Podospora is a treasure chest. I agree, not only because of the quirky aspects of its life cycle and genome biology. But also because of the amazing amount of knowledge produced by talented Podosporologists since the 60s to the present. This paper6 was a truly collaborative effort between the teams in Uppsala, Wageningen and Bordeaux, and together we stand on the shoulders of giants from the past.

Curious about the details? Check out our paper here.

Drawings by me. 

The picture of P. anserina growing on a plate in geometric shapes was taken by the Bordeaux team.

References

  1. van der Gaag, M. Genomic conflicts in Podospora anserina. PhD thesis, Wageningen Universiteit (2005).
  2. Eizaguirre, C., Lenz, T. L., Traulsen, A. & Milinski, M. Speciation accelerated and stabilized by pleiotropic major histocompatibility complex immunogenes. Ecology Letters 12, 5–12 (2009).
  3. Chevanne, D. et al. Identification of the het-r vegetative incompatibility gene of Podospora anserina as a member of the fast evolving HNWD gene family. Current Genetics 55, 93–102 (2009).
  4. Vogan, A. A. et al. Combinations of Spok genes create multiple meiotic drivers in Podospora. Elife 8, e46454 (2019).
  5. Vogan, A. A. et al. The Enterprise, a massive transposon carrying Spok meiotic drive genes. Genome Research 31, 789–798 (2021).
  6. Ament-Velásquez, S. L. et al. Allorecognition genes drive reproductive isolation in Podospora anserina. Nature Ecology & Evolution.

 

S. Lorena Ament-Velásquez

Postdoc, Stockholm University