Why is sex overwhelmingly successful? Most eukaryotes are reproducing sexually with high rates of outcrossing. Why so, if asexual reproduction provides a more straight-forward possibility to reproduce without all negative consequences associated with sex, like eg. demographic disadvantages of producing males, sexually transmitted diseases, transmission disadvantages (see Lehtonen et al 2012). This is the basic question the projects revolve around.
Transposable element evolution under asexuality
Some theories propose that asexuals are driven to extinction by a pile-up of deleterious mutations. Major drivers of the mutational meltdown might be self-replicating, deleterious transposable elements (TEs). Increased accumulation of TEs was observed for non-recombining genome portions in sexual organisms (e.g. Y-chromosomes) as a consequence of reduced effectiveness of purifying selection. However, recent findings suggest that such an accumulation does not extend to the genome scale of asexual arthropods (Bast et al. 2015). One explanation might be that TEs evolve to be benign (i.e. less active and/or harmful), as host and TE fates are coupled in completely asexual genomes. This was done in close collaboration with Ken Kraaijeveld.
We currently use a more extensive phylogenetic framework of asexual and closely related sexual species with young to ancient time scales of asexuality, including (Timema (5 pairs), oribatid mites (2 pairs) and darwinulid ostracods (1 pair), to generate more insights into TE evolution in sex vs asex, including TE activity and polymorphism.
Additionally, we followed up on the ‘benign TEs’ idea. We compared TE dynamics of sexual and asexual yeast lineages through time. And actually, asexuality drives the reduction of TE load, consistent with theory (read preprint here).
Consequences of asexuality in natural populations
Here, we use orthologous expressed genes in 5 sex-asex pairs of Timema stick insects to empirically test, if predicted consequences for genome evolution under asexuality can be found in the wild. Turns out, they do for Timema (other than mites). Asexual Timema are under less effective purifying selection at both segregating variants and in the long-term, have lower genetic variation and arrested GC biased gene conversion as compared to sexual sisters. Check out the paper here.
In a large-scale genome project involving 3 working groups, we sequenced these 10 genomes and population samples. We are currently investigating heterozygosity, horizontally transferred genes, genome structure and TE content of these 5 sex-asex pairs.
Purifying selection in ancient asexuals
There is little agreement over which mechanisms are able to generate selection for sex in natural populations on the short-term. However, it is established consensus that sex and recombination are beneficial for the long-term persistence of lineages, because asexuals theoretically will experience mutational meltdown. There is empirical support for deleterious mutation accumulation in the absence of recombination as a result of less efficient purifying selection in natural populations of young asexual lineages.
However, some animals seem to persist in the absence of sex (such as oribatid mites), and it is currently unknown if these can avoid accumulation of deleterious point mutations. Using six oribatid mite transcriptomes and an extended taxon sampling with two genes, we infered the accumulation of point mutations and selection on codon usage between sexuals and asexuals. There seems no evidence for impeded selection in asexual lineages and surprisingly, our results suggest even more effective purifying selection in asexual oribatid mites and imply that these asexuals escape mutational meltdown. As the effectiveness of purifying selection is influenced not only by reproductive mode, but also population sizes, the findings might be a consequence of the massive number of asexual mites.
Future directions: Persistence in absence of sex
Understanding the genomic substrate for persistence without sex.
We generate and analyse genomes and transcriptomes of mites, consisting of asexual and closely related sexual species. We test if allelic sequences diverge, estimate a time-frame of asexuality, check for signatures of events of recombination, how effective purifying selection can be maintained, nucleotide landscape evolution, transposable element dynamics, overall genome structure and mechanisms that generate evolvability. Moreover, we use mite lineages that ecologically diverged into species, to understand how asexual speciation is achieved.