Asexual reproduction drives the reduction of transposable element load

Transposable elements (TEs) are able to proliferate in genomes via different self-copying mechanisms. Theory predicts that sexual reproduction can both facilitate and restrain TE accumulation by respectively providing TEs with a means of spreading to all individuals in a population and facilitating TE load reduction via purifying selection. By quantifying genomic TE loads over time in experimental sexual and asexual yeast populations, we provide direct evidence that asexual reproduction drives a reduction of genomic TE loads. We show, using simulations, that this reduction occurs via evolution of TE activity, most likely via increased excision rates. Our study thus demonstrates that sexual reproduction is a major driver of TE loads and at the root of the success of TEs. One Sentence Summary Sexual reproduction is at the root of the success of parasitic TEs

accumulation by respectively providing TEs with a means of spreading to all individuals in a population and facilitating TE load reduction via purifying selection. By quantifying genomic TE loads over time in experimental sexual and asexual yeast populations, we provide direct evidence that asexual reproduction drives a reduction of genomic TE loads. We show, using simulations, that this reduction occurs via evolution of TE activity, most likely via increased 20 excision rates. Our study thus demonstrates that sexual reproduction is a major driver of TE loads and at the root of the success of TEs.
One Sentence Summary: 25 Sexual reproduction is at the root of the success of parasitic TEs Main Text: 30 Self-replicating transposable elements (TEs) can occupy large fractions of genomes in organisms throughout the tree of life (reviewed in (1)). Their overwhelming success is driven by their ability to proliferate independently of the host cell cycle via different self-copying mechanisms (i.e., in a 'cut-and-paste' or 'copy-and-paste' style). These mechanisms allow TEs to invade genomes similarly to parasites despite generally not providing any advantage to the individual 35 carrying them (2, 3). To the contrary, TEs generate deleterious effects in their hosts by promoting ectopic recombination and because most new TE insertions in coding or regulatory sequences disrupt gene functions (4,5).
Theory predicts that sexual reproduction can both facilitate and restrain the genomic accumulation of TEs and it is currently unclear whether the expected net effect of sex on TE 40 loads is positive or negative. Sexual reproduction can facilitate the accumulation of TEs because it allows TEs to colonize new genomes and spread throughout populations (6,7). Because the colonization of new genomes is more likely for active TEs, sexual reproduction should favor the evolution of highly active TEs (6,8), even though increased activity generates higher TE loads and additional deleterious effects in the host genome. At the same time, sexual reproduction can 45 restrain TE accumulation because it facilitates the evolution of host defences and increases purifying selection against deleterious TE copies (9)(10)(11)(12)(13). In the the absence of sex, reduced purifying selection can thus result in the accumulation of TEs, unless TE copies get eliminated via excision at sufficiently high rates (14).
To quantify whether the net effect of sexual reproduction on genomic TE loads is positive or 50 negative, we study the evolution of genomic TE loads in experimental yeast (Saccharomyces cerevisiae) populations generated in a previous study (15). In this study, four sexual and four asexual strains originating from the same ancestor strain (W303) were maintained under constant conditions. For sexual strains, a mating event was induced every 90 generations. Sequencing of each strain was conducted at generation 0 and every 90 generations prior to mating (for details 55 see Supplementary Materials, and (15)). In the present study, we use the published Illumina data to quantify TE loads in each strain for each sequenced generation.
TEs in S. cerevisiae are well characterized and this yeast does not have the TE silencing machineries known in other fungi (16)(17)(18). S. cerevisiae TEs consist solely of 'copy-and-paste' elements that are flanked by long terminal repeats (LTRs) and are grouped into the families Ty1-60 Ty5 (16). The 12.2 Mb genome of the studied yeast strain comprises approximately 50 fulllength, active Ty element copies, and 430 inactive ones (17). Inactive copies comprise truncated elements as well as remnants from TE excisions, which consist of a single LTR (17). Excisions are driven by intra-chromosomal recombination between the two flanking LTRs of a TE.
Using different computational approaches to quantify genomic TE loads in experimental yeast 65 strains, we show that sex is required for the success of TEs, as TE loads decrease over time under asexual reproduction. For the first approach, we quantified total TE loads, without distinguishing between active and inactive TEs. This was done by computing the fraction of reads that mapped to a curated S. cerevisiae TE library (see Supplementary Materials) for each yeast strain and sequenced generation. This analysis revealed that the total TE load in sexual 70 strains remained constant over 1000 generations, but decreased in asexual strains over time (resulting in a total reduction of 23.5% after 1000 generations; generation effect P < 0.001, reproductive mode effect P = 0.081, and interaction between generation and mode P < 0.001; permutation ANOVA, Fig. S1). For the second approach, we focused on active (i.e., full-length) TE copy insertions, because only active TEs can increase genomic TE loads over time. Detecting 75 specific TE insertions by aligning short-read data to a reference genome is difficult and associated with a detection bias towards TEs present in the reference genome. With a pipeline that combines different complementary approaches (see Supplementary Materials), the available sequencing data allowed us to detect 24 out of the 50 insertions present in the reference genome. As with the first approach, we found that the number of (detectable) full-length TE 80 copies remained constant in sexual yeast strains, but decreased in asexual strains over time (generation effect P = 0.006, reproductive mode effect P = 0.033, and interaction between generation and mode P < 0.001; permutation ANOVA). In asexual strains, the estimated average number of full-length TEs decreased from approximately 50 to 41 over 1000 generations (Fig.   1A). Taken together, our empirical observations indicate that even very rare events of sex (here 85 just 10 out of 990 events of reproduction) are sufficient to maintain genomic TE loads, while asexuality results in the reduction of TE loads. In a second step, we wanted to identify the mechanisms that explain why genomic TE loads in 100 experimental yeast strains decrease in the absence of sexual reproduction. As explained above, different theoretical approaches have shown that specific mechanisms can affect TE loads under sexual or asexual reproduction, sometimes with opposite effects (6,8,14). However, there is currently no theoretical framework that studies TE load evolution under the joint effects of the different mechanisms. To fill this gap, we extended the individual-level simulation program of 105 Dolgin and Charlesworth (14). This program allows to study the evolution of TE copy numbers in an asexual lineage as a function of TE activity (the joint effects of transposition and excision rates), as well as of the strength of selection against TE insertions, which depends on the fitness cost per TE insertion. To compare TE loads in sexual and asexual lineages, we first extended the program to include events of sexual reproduction and parameterized the simulations with 110 empirically determined values from yeast (17,19,20) (see Supplementary Material). We thus ran individual-based simulations with a range of transposition rates, excision rates and selection coefficients with and without epistasis between TE copies as pertinent for yeast (see Table S2).
For all simulations, TE loads in populations undergoing sex every 90 generations decreased faster than in asexual populations, contrary to our empirical observations. This faster decrease of 115 TE loads in sexual populations occurred because sexual events generated variation among individuals in TE loads (i.e., fitness), which facilitates selection against deleterious TEs (see also (14)). We therefore further extended the theoretical framework to allow for TE activity rate evolution by introducing a modifier allele that increases excision rates. The allele itself has no direct fitness effect, such that it can only be fixed in a population via genetic hitchhiking. In 120 simulations including the modifier allele, the modifier spreads rapidly to fixation in asexual strains, because it is associated with genomes that have fewer TE copies and therefore a higher relative fitness. As a consequence, TE activity rates decrease in asexual populations (Fig. S3).
By contrast, the modifier cannot spread as rapidly in sexual populations because recombination constantly breaks up the association between the modifier and less TE loaded backgrounds. By 125 allowing for the evolution of TE activity rates in our simulations, we were able to identify parameter values representative for yeast that result in simulations with a very close fit to our empirical results (Fig. 1B, Table S3). These findings thus suggest that a likely mechanism driving genomic TE load reduction in asexual yeast strains is the rapid evolution of increased TE excision rates. A similar effect would be expected if our modifier acted on transposition rather 130 than excision rates, since the net TE activity depends on the relative rates of transposition vs excision. The available data for the experimental yeast strains does not allow for the evaluation of these mutually non-exclusive effects, as such a distinction would require the reliable identification of most specific insertion sites of TEs at different generations. But given our findings that in the absence of TE activity evolution, sexual strains always lose TEs faster than 135 asexual ones, the empirical findings are best explained by a change in TE transposition or excision rates under asexuality.
Our study conclusively shows that sexual reproduction drives the maintenance of TE load in S. cerevisiae, while in its absence, TE loads decrease, likely via the evolution of TE activity rates.
These findings are consistent with the idea that TEs should evolve to be benign in asexual 140 species, because the evolutionary interests of TEs and their host genome are aligned (8). While the exact mechanisms causing TE activity change in the asexual yeast populations cannot be assessed in the empirical data, our simulations suggest that there is some form of TE defense mechanism (a 'modifier locus') that either segregates in the ancestral yeast strain used in the experiments or repeatedly appeared de novo during experimental evolution. Independently of the 145 exact mechanism underlying TE activity evolution in asexual populations, we show that TE loads do not increase, but decrease, in asexual populations. This contrasts with the hypothesis that most asexual species are evolutionarily short lived because they are driven to extinction via negative consequences of accumulating TE copies (9,13). Instead, sex, which is the main form of reproduction in eukaryotes, is at the root of the evolutionary success of parasitic TEs.

Yeast experimental evolution
We used data generated in a previous study based on experimental evolution of the yeast S.
cerevisiae (for in-depth details see (15)). In short, 12 different strains were initiated from the 240 same pool of ancestral strains (derived from haploid W303 strains) and kept under constant conditions. Sexual reproduction in yeast depends on the presence of two separate mating types. To identify full-length TEs and solo LTR insertions, we tagged insertions by length according to the typical TY TE properties found in S. cerevisiae (i.e. a full TE is a combination of internal sequence and two LTRs within a 500 bp range; solo LTRs are between 220 and 420 bp; see table S1). Because TE insertion detection was influenced by coverage, it had to be taken into account for calculating the number of insertions, by adding coverage as random factor (coverage effect P 295 < 0.001, generation effect P = 0.006, reproductive mode effect P = 0.033, and interaction between generation and mode P < 0.001; permutation ANOVA). We then calculated the number of lost TEs in asexual strains from the regression slope in asexuals after correcting for coverage (residuals) over 1000 generations, assuming 50 full-length TEs in the ancestor.  Table S2). We further explored the effects of different transposition rates during meiosis vs asexual reproduction, but this did not change the dynamics even for meiotic 320 transposition rates that were not biologically relevant (up to 0.1, i.e. 10% of TEs have transposed during meiosis). The last extension included the introduction of an unliked, general modifier allele increasing the excision rates. The parameters related to this extension are the initial frequency of the modifier allele and the excision rate increases when the modifier allele is present (see Table S3). See the code documentation for details. 325 Code availability The code used for both the analyses of empirical data and for the theoretical prediction of TE dynamics together with explanations are available online at https://github.com/KamilSJaron/reproductive_mode_TE_dynamics 330 Fig. S1. Transposable element load remains stable in sexual strains, but is reduced in asexual strains after 1000 generations. Read fraction mapping to TEs relative to the sum of reads mapping to the genome and/or the TE library for each of the four replicate sexual (red) and asexual (blue) strains sequenced every 90 generations (from generation 0 to 990).  S3. The spread of a modifier of excision rates is faster in asexual than sexual populations because it remains linked to genomes that have few TE copies and therefore a high relative fitness. The modifier allele frequency is shown over time for simulations under sexual (red) and asexual (blue) reproduction, with ten replicates.  Table S3. Explored parameter space for simulations including a modifier allele. Highlighted is the simulation closest to empirical observations. Init_f is the frequency of the modifier at the start of the simulations. Selection_a and selection_b are selection coefficients for linear fitness 380 effects and epistasis, respectively. Lost_TEs refers to the total number of TE lost after 1000 generations (averaged over ten replicates). The bold lines refer to parameter combinations that generate results close to the observed empirical values.