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. ↩
This easter I have spent on thinking / writing / editing of an introduction to the paper about smudgeplot - a tool for predicting ploidy and visualization of genome structure. I collaborated on this tool for my own data, I have not really thought through how far it goes, so I started to wonder how many polyploid species are out there. So I asked on Twitter and guess what, so many people have responded to the tweet that I have decided to compile the answers in a blogpost.
I was on my way back from Arthropod Genomics Symposium (which was a great conference by the way). The plan was to change planes in Iceland and get home in one go, but my flight to Iceland got delayed and I missed my connection. Fortunately, Iceland is amazing country and even around Reykjavik there is plenty to see. I decided to go to Perlan, a museum of Iceland natural history. I was shocked to hear that the island did not exist more than couple of millions years ago. I did not manage to remember the numbers, so I will take them from this web, where they say that the oldest rock is ~15 ml. Alright, 15 millions is not that little from the perspective of population genetics, enough time to generate some variability. However, we should also consider that the land was fully covered by ice during 30 rounds of glacial periods and the last time whole Iceland was under ice is 13,000 to 10,000 years ago. That means that all (or at least the most of) the macro life have started back then either as:
tiny population that survived glaciation period (bottleneck).
At the beginning of December 2017 we have decided to do a meta-study/review of several published genomes. I optimistically started to collect data for some supplementary analyses. But then I found that about one fifth of genomes were were available “on request” and about one third of genomes were missing sequencing reads. It was a shock for me, I thought that every paper needs to deposit data to DDBJ / EMBL-EBI / NCBI. This was also the case for genomes published in journals that actually claim that data need to be accessible as PloS Biology.