The analyzed species varied greatly in cellular mechanisms of asexuality (colour); ploidy levels (the black points) and origin of asexuality (not in the Figure). The black triangles are possible single origins of asexuality
Using argument of Birky 1996, assuming negligible amounts of gene conversion, old mitotic “blue” asexuals are expected to carry a lot of heterozygosity bacause of mutations independently accumulated in both (all) of the haplotypes. However, we found no such pattern. Instead of that, all the variability of the dataset was explained by the hybrid origin - regardless of the cellular mechanism. The heterozygosity is shown on the next Figure using the same colour scheme and categorization by origin of asexuality
Fascinating, there are at least three species that should lose heterozygosity over time due to recombination during meiosis. Diploscapter pachys, D. coronatus and Panagrolaimus davidi (the two orange and the pink dots on right up). Assuming that literature is right about them being meiotic asexuals there is only one possible explanation - they do not recombine (or recombination is rare and only at the sides of the chromosome(s)2. However, why they don’t recombine? Maybe it’s just the divergence of haplotypes that physically prevents the recombination. However, this would not explain how comes that all of the hybrid asexuals are heterozygous. My speculation is that these are actually f1 hybrids, they carry full gene sets of both parental species, any loss of heterozygosity must be a process deleterious to fitness. Now imagine the freshly founded asexual population where a small fraction of individuals have lower recombination rates than others. Selection will select for lowly recombining individuals because their offspring will just do better than offspring of happily recombining competitors. So I suspect that recombination will just very fast get selected out.
This ideas are sort of consistent with hybrid zones of sexual species. F1 crosses hardly ever show any lowered fitness in comparison to parents, it’s backcrosses that are crewed up… But unlike sexual hybrids, asexual do not have to backcross and therefore I see there this open space for selection against recombination.
So why are there asexual is no heterozygosity at all? Well, absence of recombination and segregation does make selection harder, we all know it from sex chromosomes. Gene conversion (or any force that homogenize haplotypes) can help fight this detrimental process as it was theoretically shown on Y chromosome. Maybe if the species starts homozygous already, the heterozygosity advantage is not so significant in contrast to benefit to avoid Muller’s ratchet by gene conversion. Obviously this is a superspeculation given my data; I would need some non-hybrid mitotic species or compare plenty of meiotic asexuals that are or are not of hybrid origin - the amount of available data is still bit limited. I suspect that with increasing number of asexual genomes sequenced we will soon find if this pattern fails as well or not.
Genome structure of polyploids
We also estimated different types of heterozygosity in the polyploid species. I though, that in autopolyploid (by whole genome duploication) one should expect an approximately event distribution of divergence between the three haplotypes, on the other hand allopolyploid species (of a hybrid origin) will display very uneven distribution with some of the chromosomes being closely related, “sexual like”, and some other being very diverged - those that have diverged during speciation. I charted this idea like this
Well, now let’s take a look what is the actual genome structure of polyploids in the dataset
Basically, rotifers must be of a hybrid origin (assuming my logic is correct). Meloidogyne are weird, but consistent - all of them have a single haplotype substantially diverged, but quite a lot of divergence between the other two or three haplotypes as well. It would be nice to have the genomes phased… The only Meloidogyne that stands out is floridensis. It have two almost identical haplotypes and a single diverged one (however far less diverged thatn in the cases of the other Meloidogyne). I would not be surprised if it would be of completely independent origin of asexuality (got to give credit to Dave Lunt for some of these thoughts). And finally with crayfish it’s hard to say. Since the variants are not phased it’s impossible to say if it’s one haplotype only diverged (in tetraploid case it’s surprisingly easier). I don’t know, what do you think. Is the crayfish a hybrid??
This study was a great fun for me. The only frustrating part I had was with collecting data (a previous blog about it), but in the end many of the authors actually fixed the data and/or uploaded them to databases, so in the end it was actually quite alright. While analyzing genomes I had a need to extend the available genome analysis tools by development of smudgeplot, which started a great great (still ongoing) collaboration with Rhyker.
I have three takehomes from this study and dicssions
Never underestimate the role of hybridization (it’s everywhere and very impactful)
The question “Can we very theoretical predictions about consequences of asexuality in natural populations?” is probably easy to answer - nope. If all the assumptions of the models are correct, none of the asexual lineages would exist. We could rather ask “What peculiarity is in this asexual lineage, so it could survive for millions of years?”
Development of a bioinformatic tool is way easier if you do it for your dataset. Instead of showing a toy data I always showed the examples from my study and people immediately seen the point. I also feel it helped me tons with meeting amazing number of incredible people. Smudgeplots rulez!
There are couple more things I am considering to write about
Genome structure of A. riciae - the very diverged haplotypes detected in the assembly can not be an artifact, the genome structure I detect either (I detect three peak kmer spectra with many many tetraploid loci) - all this suggest octoploidy but genome size measured by flow cytometry is just way too small.
Super peculiar repetitive content of P. virginalis (probably unrelated to asexuality) and why do I think it’s of a hybrid origin too even there is a decade of literature speculating otherwise.
If you would be interested, let me know, it might help my motivation.
We used an extended version of GenomeScope for estimates of heterozygosity, Smudgeplot for estimates of ploidy and DNApipeTE to estimate transposons. I declare a conflict of interest - I am a developer of smudgeplot. ↩
Both Diploscapter species are actually unichromosomal organisms. ↩
Once per while there is a new way how to do things and speed up computations in the world of kmer genomics. Sometimes the tricks are simply more efficient algorithms, but sometimes the tricks are shortcuts that don’t do excatly the same thing. Here I would like to dig a bit in the relatively new k-mer counter FastK and compare it with my personal favourite KMC. If you are wondering if it is worth learning new tool, this blogpost might be able to help you make your mind.
Few days ago, the world learned about two California condor chicks that were products of parthenogenesis, a reproduction where unfertilised eggs hatch and develop in an adult from maternal genome only. This IS exciting for multiple reasons, but perhaps not as exiting for conservation of condors and I will try to explain why… It will take a bit of background on parthenogenesis and sex determination, but bear with me.
When I was young naive aspiring scientist I did not comprehend all the aspects of publishing. To be honest, I did not think about it much, but for me it’s the same as the climate change, it’s harder and harder to turn a blind eye. The last drop for me was the announcement of Nature’s Open Access option, it’s shocking €9,500, (or $11,390 / £8,290)! How did we come to this? Are we really going to let a private company to drain the already poor scholarly funds by these obscure amounts? And the problem is not just Nature…
About a year and half ago an article by John Tregoning was published in Nature News. The short piece was openly defending the prevalent usage of journal impact factor for evaluation of junior scientists for their sake. As a junior scientist I felt bitter. The publishing system is a huge academic problem we should do something about it! And as far as I know, young scientists are the loudest in pointing out new ways for less morally corrupted sharing of knowledge and therefore I find unfair a senior academic takes us, as an argument for keeping the status quo.