The answer
You probably need large population sizes and independent haplotype evolution
...for effective selection and generation of novelty in the absence of sex.
Read on to know more...
Read on to know more...
This is Platynothrus peltifer.
These all-female Oribatid mite lineages are very special as they happily reproduce without sex for millions of years.
These all-female Oribatid mite lineages are very special as they happily reproduce without sex for millions of years.
We know from previous studies that they do not have problems with effective purifying selection (Brandt et al 2017 and Bast et al 2016).
How can they escape extinction while others can not?
Are there specific genome dynamics that might help to adapt and diversify in the absence of sex?
To find out we go into forests and sample natural populations. These oribatid mites are tiny (<<1mm), mostly decomposers and we can not keep them in lab rearings (as generation times are 1 year). So to generate insights into "the genomic substrate for persistence without sex", we needed to generate high quality genomes from SINGLE INDIVIDUALS.
Hünsa Öztoprak, Shan Gao, Nadège Guiglielmoni et al succeeded!
Actually better than expected:
Actually better than expected:
A chromosome-level, high quality, phased assembly where all sequence information stems from a single individual (we cheated a bit with Hi-C and pooled a bunch to scaffold to chromosome scale).
A diploid (2n=18) genome with expected 220 MB in size. You can see that haplotypic blocks are nicely phased (93% of the genome).
A diploid (2n=18) genome with expected 220 MB in size. You can see that haplotypic blocks are nicely phased (93% of the genome).
Now we can ask: Is there independent haplotype evolution (aka the 'Meselson effect')
In diploid, effectively clonal asexuals, haplotypes diverge independently over time without gene flow. So transition to asexuality happened before population separationh, haplotype trees should split haplotypes first and then populations creating mirror-image haplotype trees.
There is very scarce empirical evidence for this prediction. Well, but one is from the mites (see Brandt et al. 2021).
There is very scarce empirical evidence for this prediction. Well, but one is from the mites (see Brandt et al. 2021).
We sampled five populations worldwide and generated phased data.
Mean heterozygosity between haplotypes within individuals for each population. All populations show similar patterns of heterozygosity along chromosomes. JP and CA show a lower mean but no localized stretches of loss of heterozygosity, which suggests lower overall mutation rates for JP and CP.
And we found the Meselson effect again, this time on the haplotypic block scale!!
Using divergence between haplotypes, empirical estimates of spontaneous mutation rates and gene conversion track lengths, we simulated heterozygosity gain over time. We found that P. peltifer is reproducing asexually for at least 20 my!
Using divergence between haplotypes, empirical estimates of spontaneous mutation rates and gene conversion track lengths, we simulated heterozygosity gain over time. We found that P. peltifer is reproducing asexually for at least 20 my!
— How do independent haplotypes contribute to evolvability?
We checked about 10000 1:1 allelic orthologs for sequence differences, differential expression and horizontally transferred genes and transposable elements and found indications for allele-specific selection and sources for novelty (check also Posters 241 and 861). See specifics here:
We checked about 10000 1:1 allelic 'orthologs' for differences. About 90% of alleles differ to each other with synonymous and nonsynonymous variants and about 10% gained or lost a stop codon and 10% show frameshifts. Ka/Ks analysis suggests allele-specific direction of selection with 5% of alleles showing signs of strong positive selection (Ka/Ks>1).
Differentially expressed alleles are under selection. About 9% (936) of alleles are differentially expressed. These DEA are more different to each other than equivalently expressed alleles (EEA) and the differences are only found in the exons, suggesting selective processes driving the difference in gene content and expression.
HGTs contribute to novelty. In total we found 2% (504) HGT genes in the P. peltifer genome. Allelic HGT are more different to each other than non-HGT genes and 3% are differentially expressed. These differences can be nucleotide and structural variants (like an exon missing). 6.5% (33) of HGTs are 'orphan', i.e. only one copy on one haplotype is found. These arrived likely after the transition to asexuality. HGT genes are enriched for function that have a connection with resources.
About 20% TEs are found in the P. peltifer genome. TEs show purifying selection in genic regions. Notabliy, TEs have a slight but noticeable difference in their historical activity between haplotypic blocks.
Overall, our findings suggest that haplotypic independence likely contributes to evolvability and persistence without sex
For more ancient mite stories check posters about:
Speciation under asexuality (267)
Transposable elements (866)
DEA and HGT for novelty (239)
Sex determination (794)
Speciation under asexuality (267)
Transposable elements (866)
DEA and HGT for novelty (239)
Sex determination (794)
Thanks to the DFG for funding our research!
The Funding:
Our work is generously funded by the DFG Emmy Noether fellowship BA 5800/3-1 (to J.B.)
Feel free to chat with me
Jens Bast
Principal investigator or the "Sex Lab"
Here at the SMBE or
Email: jbast@uni-koeln.de
Email: jbast@uni-koeln.de
