Many organisms across the Tree of life have the ability to produce seeds, eggs, cysts, or spores, that can remain dormant for several generations before hatching. This widespread adaptive trait in bacteria, fungi, plants and animals, has a significant impact on the ecology, population dynamics and population genetics of species that express it (Evans and Dennehy 2005).

In population genetics, and despite the recognition of its evolutionary importance in many empirical studies, few theoretical models have been developed to characterize the evolutionary consequences of this trait on the level and distribution of neutral genetic diversity (see, e.g., Kaj et al. 2001; Vitalis et al. 2004), and also on the dynamics of selected alleles (see, e.g., Živković and Tellier 2018). However, due to the complexity of the interactions between evolutionary forces in the presence of dormancy, the fate of selected mutations in their genomic environment is not yet fully understood, even from the most recently developed models.

In a comprehensive article, Korfmann et al. (2023) aim to fill this gap by investigating the effect of germ banking on the probability of (and time to) fixation of beneficial mutations, as well as on the shape of the selective sweep in their vicinity. To this end, Korfmann et al. (2023) developed and released their own forward-in-time simulator of genome-wide data, including neutral and selected polymorphisms, that makes use of Kelleher et al.’s (2018) tree sequence toolkit to keep track of gene genealogies.

The originality of Korfmann et al.’s (2023) study is to provide new quantitative results for the effect of dormancy on the time to fixation of positively selected mutations, the shape of the genomic landscape in the vicinity of these mutations, and the temporal dynamics of selective sweeps. Their major finding is the prediction that germ banking creates narrower signatures of sweeps around positively selected sites, which are detectable for increased periods of time (as compared to a standard Wright-Fisher population).

The availability of Korfmann et al.’s (2023) code will allow a wider range of parameter values to be explored, to extend their results to the particularities of the biology of many species. However, as they chose to extend the haploid coalescent model of Kaj et al. (2001), further development is needed to confirm the robustness of their results with a more realistic diploid model of seed dormancy.

REFERENCES

Evans, M. E. K., and J. J. Dennehy (2005) Germ banking: bet-hedging and variable release from egg and seed dormancy. The Quarterly Review of Biology, 80(4): 431-451. https://doi.org/10.1086/498282

Kaj, I., S. Krone, and M. Lascoux (2001) Coalescent theory for seed bank models. Journal of Applied Probability, 38(2): 285-300. https://doi.org/10.1239/jap/996986745

Kelleher, J., K. R. Thornton, J. Ashander, and P. L. Ralph (2018) Efficient pedigree recording for fast population genetics simulation. PLoS Computational Biology, 14(11): e1006581. https://doi.org/10.1371/journal.pcbi.1006581

Korfmann, K., D. Abu Awad, and A. Tellier (2023) Weak seed banks influence the signature and detectability of selective sweeps. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.04.26.489499

Vitalis, R., S. Glémin, and I. Olivieri (2004) When genes go to sleep: the population genetic consequences of seed dormancy and monocarpic perenniality. American Naturalist, 163(2): 295-311. https://doi.org/10.1086/381041

Živković, D., and A. Tellier (2018). All but sleeping? Consequences of soil seed banks on neutral and selective diversity in plant species. Mathematical Modelling in Plant Biology, 195-212. https://doi.org/10.1007/978-3-319-99070-5_10

The ability of a population to adapt to a new niche is an important phenomenon in evolutionary biology. The colonisation of a new volcanic island by plant species; the colonisation of a host treated by antibiotics by a-resistant strain; the Ebola virus transmitting from bats to humans and spreading epidemically in Western Africa, are all examples of a population invading a new niche, adapting and eventually establishing in this new environment.

Adaptation to a new niche can be studied using source-sink models. In the original environment —the “source”—, the population enjoys a positive growth-rate and is self-sustaining, while in the new environment —the “sink”— the population has a negative growth rate and is able to sustain only by the continuous influx of migrants from the source. Understanding the dynamics of adaptation to the sink environment is challenging from a theoretical standpoint, because it requires modelling the demography of the sink as well as the transient dynamics of adaptation. Moreover, local selection in the sink and immigration from the source create distributions of genotypes that complicate the use of many common mathematical approaches.

In their paper, Lavigne et al. [1], develop a new deterministic model of adaptation to a harsh sink environment in an asexual species. The fitness of an individual is maximal when a number of phenotypes are tuned to an optimal value, and declines monotonously as phenotypes are further away from this optimum. This model —called Fisher’s Geometric Model— generates a GxE interaction for fitness because the phenotypic optimum in the sink environment is distinct from that in the source environment [2]. The authors circumvent mathematical difficulties by developing an original approach based on tracking the deterministic dynamics of the cumulant generating function of the fitness distribution in the sink. They derive a number of important results on the dynamics of adaptation to the sink:

• From the point where immigration from the source to the sink starts, four phases of adaptation are observed. After a short transient phase (phase 1), a migration-selection balance is reached in the sink (phase 2). After a while, thanks to the immigration of rare adapted migrants and mutation in the sink, a small fraction of the sink population exhibits a close-to-optimal phenotype. This small adapted fraction grows in frequency and mean fitness rapidly increases in the sink (phase 3). Finally, the population settles around the sink optimum (phase 4) and, hurray, the sink is now a source!

• Interestingly, in this model the evolutionary dynamics do not depend on the immigration rate. In other words, adaptation will proceed at the same rate regardless of how many immigrants invade the sink. This is because the impact of immigration on adaptation depends on the rate of immigration relative to the sink density. This ratio is actually independent of immigration in a model where the sink is initially empty, migration from the sink back to the source is negligible and without density-dependence in the sink.

• In this model, mutation is a double-edged sword. Adapted phenotypes emerge from new mutations, and under this effect alone a higher mutation rate would translate into a shorter time to establishment in the sink. However, mutations may also have deleterious effects by displacing the phenotype away from the optimum. This mutation load will be greater when individuals need to simultaneously tune a large number of phenotypes. As a consequence of these two effects of mutations, time to establishment is minimal for an intermediate mutation rate. This result emerges from Fisher’s Geometric Model, but may hold more generally for biologically plausible fitness landscapes where mutations generates both beneficial (allowing adaptation to the sink) and deleterious genotypes.

• Lastly, in Fisher’s Geometric Model, the time to establishment increases superlinearly with harshness of the sink when the sink is too harsh, and establishment may occur only after a very long time. In these harsh sinks, the adapted genotypes are very few and increase very slowly in frequency, making the second phase of adaptation much longer. Thus, and as a direct consequence of Fisher’s Geometric Model, adding a “stepping stone” intermediate environment would allow faster adaptation to the extreme environment.

In conclusion, this theoretical work presents a method based on Fisher’s Geometric Model and the use of cumulant generating functions to resolve some aspects of adaptation to a sink environment. It generates a number of theoretical predictions for the adaptive colonisation of a sink by an asexual species with some standing genetic variation. It will be a fascinating task to examine whether these predictions hold in experimental evolution systems: will we observe the four phases of the dynamics of mean fitness in the sink environment? Will the rate of adaptation indeed be independent of the immigration rate? Is there an optimal rate of mutation for adaptation to the sink? Such critical tests of the theory will greatly improve our understanding of adaptation to novel environments.

References

[1] Lavigne, F., Martin, G., Anciaux, Y., Papaïx, J., and Roques, L. (2019). When sinks become sources: adaptive colonization in asexuals. bioRxiv, 433235, ver. 5 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/433235
[2] Martin, G., and Lenormand, T. (2006). A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species. Evolution, 60, 893-907. doi: 10.1111/j.0014-3820.2006.tb01169.x

Cytoplasmic incompatibility (CI) is a mating incompatibility that is induced by maternally inherited endosymbionts in many arthropods. These endosymbionts include, most famously, the alpha-proteobacterium Wolbachia pipientis (Yen & Barr 1971; Werren et al. 2008) but also the Bacteroidetes bacterium Cardinium hertigii (Zchori-Fein et al. 2001), a gamma-proteobacterium of the genus Rickettsiella (Rosenwald et al. 2020) and another, as yet undescribed alpha-proteobacterium (Takano et al. 2017). CI manifests as embryonic mortality in crosses between infected males and females that are uninfected or infected with a different strain, whereas embryos develop normally in all other crosses. This phenotype may enable the endosymbionts to spread rapidly within their host population. Exploiting this, CI-inducing Wolbachia are being harnessed to control insect-borne diseases (e.g., O'Neill 2018). Much progress elucidating the genetic basis and developmental mechanism of CI has been made in recent years, but many open questions remain (Shropshire et al. 2020).
Immediately following the discovery and early study of CI in mosquitoes, Laven (1959, 1967) proposed that CI could be an important driver of speciation. Indeed, bi-directional CI can strongly reduce gene flow between two populations due to the elimination of F1 embryos, so that CI can act as a trigger for genetic differentiation in the host (Telschow et al. 2002, 2005). This idea has received much attention, and a potential role for CI in incipient speciation has been demonstrated in several species (e.g., Bordenstein et al. 2001; Jaenike et al. 2006). However, we still don’t know how commonly CI actually triggers speciation, rather than being merely a minor player or secondary phenomenon. The problem is that in addition to CI, postzygotic reproductive isolation can also be caused by host-induced, nuclear incompatibilities. Determining the relative contributions of these two causes of isolation is difficult and has rarely been done.
The study by Cruz et al. (2020) addresses this problem head-on, using a study system of Tetranychus urticae spider mites. These cosmopolitan mites are infected with different strains of Wolbachia. They come in two different colour forms (red and green) that can co-occur sympatrically on the same host plant but exhibit various degrees of reproductive isolation. A complicating factor in spider mites is that they are haplodiploid: unfertilised eggs develop into haploid males and are therefore not affected by any postzygotic incompatibilities, whereas fertilised eggs normally develop into diploid females. In haplodiploids, Wolbachia-induced CI can either kill diploid embryos (as in diplodiploid species), or turn them into haploid males. In their study, Cruz et al. used three different populations (one of the green and two of the red form) and employed a full factorial experiment involving all possible combinations of crosses of Wolbachia infected or uninfected males and females. For each cross, they measured F1 embryonic and juvenile mortality as well as sex ratio, and they also measured F1 fertility and F2 viability. Their results showed that there is strong reduction in hybrid female production caused by Wolbachia-induced CI. However, independent of this and through a different mechanism, there is an even stronger reduction in hybrid production caused by host-associated incompatibilities. In combination with the also observed near-complete sterility of F1 hybrid females and full F2 hybrid breakdown (neither of which is caused by Wolbachia), the results indicate essentially complete reproductive isolation between the green and red forms of T. urticae.
Overall, this is an elegant study with an admirably clean and comprehensive experimental design. It demonstrates that Wolbachia can contribute to reproductive isolation between populations, but that host-induced mechanisms of reproductive isolation predominate in these spider mite populations. Further studies in this exiting system would be useful that also investigate the contribution of pre-zygotic isolation mechanisms such as assortative mating, ascertain whether the results can be generalised to other populations, and – most challengingly – establish the order in which the different mechanisms of reproductive isolation evolved.

References

Bordenstein, S. R., O'Hara, F. P., and Werren, J. H. (2001). Wolbachia-induced incompatibility precedes other hybrid incompatibilities in Nasonia. Nature, 409(6821), 707-710. doi: https://doi.org/10.1038/35055543
Cruz, M. A., Magalhães, S., Sucena, É., and Zélé, F. (2020) Wolbachia and host intrinsic reproductive barriers contribute additively to post-mating isolation in spider mites. bioRxiv, 2020.06.29.178699, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. doi: https://doi.org/10.1101/2020.06.29.178699
Jaenike, J., Dyer, K. A., Cornish, C., and Minhas, M. S. (2006). Asymmetrical reinforcement and Wolbachia infection in Drosophila. PLoS Biol, 4(10), e325. doi: https://doi.org/10.1371/journal.pbio.0040325
Laven, H. (1959). SPECIATION IN MOSQUITOES Speciation by Cytoplasmic Isolation in the Culex Pipiens-Complex. In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 24, pp. 166-173). Cold Spring Harbor Laboratory Press.
Laven, H. (1967). A possible model for speciation by cytoplasmic isolation in the Culex pipiens complex. Bulletin of the World Health Organization, 37(2), 263-266.
O’Neill S.L. (2018) The Use of Wolbachia by the World Mosquito Program to Interrupt Transmission of Aedes aegypti Transmitted Viruses. In: Hilgenfeld R., Vasudevan S. (eds) Dengue and Zika: Control and Antiviral Treatment Strategies. Advances in Experimental Medicine and Biology, vol 1062. Springer, Singapore. doi: https://doi.org/10.1007/978-981-10-8727-1_24
Rosenwald, L.C., Sitvarin, M.I. and White, J.A. (2020). Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host. doi: https://doi.org/10.1098/rspb.2020.1107
Shropshire, J. D., Leigh, B., and Bordenstein, S. R. (2020). Symbiont-mediated cytoplasmic incompatibility: what have we learned in 50 years?. Elife, 9, e61989. doi: https://doi.org/10.7554/eLife.61989
Takano et al. (2017). Unique clade of alphaproteobacterial endosymbionts induces complete cytoplasmic incompatibility in the coconut beetle. Proceedings of the National Academy of Sciences, 114(23), 6110-6115. doi: https://doi.org/10.1073/pnas.1618094114
Telschow, A., Hammerstein, P., and Werren, J. H. (2002). The effect of Wolbachia on genetic divergence between populations: models with two-way migration. the american naturalist, 160(S4), S54-S66. doi: https://doi.org/10.1086/342153
Telschow, A., Hammerstein, P., and Werren, J. H. (2005). The effect of Wolbachia versus genetic incompatibilities on reinforcement and speciation. Evolution, 59(8), 1607-1619. doi: https://doi.org/10.1111/j.0014-3820.2005.tb01812.x
Werren, J. H., Baldo, L., and Clark, M. E. (2008). Wolbachia: master manipulators of invertebrate biology. Nature Reviews Microbiology, 6(10), 741-751. doi: https://doi.org/10.1038/nrmicro1969
Yen, J. H., and Barr, A. R. (1971). New hypothesis of the cause of cytoplasmic incompatibility in Culex pipiens L. Nature, 232(5313), 657-658. doi: https://doi.org/10.1038/232657a0
Zchori-Fein, E., Gottlieb, Y., Kelly, S. E., Brown, J. K., Wilson, J. M., Karr, T. L., and Hunter, M. S. (2001). A newly discovered bacterium associated with parthenogenesis and a change in host selection behavior in parasitoid wasps. Proceedings of the National Academy of Sciences, 98(22), 12555-12560. doi: https://doi.org/10.1073/pnas.221467498

Within-host parasite density is tightly linked to parasite fitness often determining both transmission success and virulence (parasite-induced harm to the host) (Alizon et al., 2009, Anderson & May, 1982). Parasite density may thus be controlled by selection balancing these conflicting pressures. Actual within-host density regulation may be under host or parasite control, or due to other environmental factors (Wale et al., 2019, Vale et al., 2011, Chrostek et al., 2013). Vertically transmitted parasites may also be more vulnerable to drift associated with bottlenecks between generations, which may also determine within-host population size (Mathe-Hubert et al., 2019, Mira & Moran, 2002).

Bénard et al. (2021) use 3 experiments to disentangle the role of drift versus host factors in the control of within-host Wolbachia growth in Drosophila melanogaster. They use the wMelPop Wolbachia strain in which virulence (fly longevity) and within-host growth correlate positively with copy number in the genomic region Octomom (Chrostek et al., 2013, Chrostek & Teixeira, 2015). Octomom copy number can be used as a marker for different genetic lineages within the wMelPop strain.

In a first experiment, they introgressed and backcrossed this Wolbachia strain into 6 different host genetic backgrounds and show striking differences in within-host symbiont densities which correlate positively with Octomom copy number. This is consistent with host genotype selecting different Wolbachia strains, but also with bottlenecks and drift between generations. To distinguish between these possibilities, they perform 2 further experiments. 

A second experiment repeated experiment 1, but this time introgression was into 3 independent lines of the Bolivia and USA Drosophila populations; those that, respectively, exhibited the lowest and highest Wolbachia density and Octomom copy number. In this experiment, growth and Octomom copy number were measured across the 3 lines, for each population, after 1, 13 and 25 generations. Although there were little differences between replicates at generation 1, there were differences at generations 13 and 25 among the replicates of both the Bolivia and USA lines. These results are indicative of parasite control, or drift being responsible for within-host growth rather than host factors. 

A third experiment tested whether Wolbachia density and copy number were under host or parasite control. This was done, again using the USA and Bolivia lines, but this time those from the first experiment, several generations following the initial introgression and backcrossing. The newly introgressed lines were again followed for 25 generations. At generation 1, Wolbachia phenotypes resembled those of the donor parasite population and not the recipient host population indicating a possible maternal effect, but a lack of host control over the parasite. Furthermore, Wolbachia densities and Octomom number differed among replicate lines through time for Bolivia populations and from the donor parasite lines for both populations. These differences among replicate lines that share both host and parasite origins suggest that drift and/or maternal effects are responsible for within-host Wolbachia density and Octomom number. 

These findings indicate that drift appears to play a role in shaping Wolbachia evolution in this system. Nevertheless, completely ruling out the role of the host or parasite in controlling densities will require further study. The findings of Bénard and coworkers (2021) should stimulate future work on the contribution of drift to the evolution of vertically transmitted parasites.

References

Alizon S, Hurford A, Mideo N, Baalen MV (2009) Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future. Journal of Evolutionary Biology, 22, 245–259. https://doi.org/10.1111/j.1420-9101.2008.01658.x

Anderson RM, May RM (1982) Coevolution of hosts and parasites. Parasitology, 85, 411–426. https://doi.org/10.1017/S0031182000055360

Bénard A, Henri H, Noûs C, Vavre F, Kremer N (2021) Wolbachia load variation in Drosophila is more likely caused by drift than by host genetic factors. bioRxiv, 2020.11.29.402545, ver. 4  recommended and peer-reviewed by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2020.11.29.402545

Chrostek E, Marialva MSP, Esteves SS, Weinert LA, Martinez J, Jiggins FM, Teixeira L (2013) Wolbachia Variants Induce Differential Protection to Viruses in Drosophila melanogaster: A Phenotypic and Phylogenomic Analysis. PLOS Genetics, 9, e1003896. https://doi.org/10.1371/journal.pgen.1003896

Chrostek E, Teixeira L (2015) Mutualism Breakdown by Amplification of Wolbachia Genes. PLOS Biology, 13, e1002065. https://doi.org/10.1371/journal.pbio.1002065

Mathé‐Hubert H, Kaech H, Hertaeg C, Jaenike J, Vorburger C (2019) Nonrandom associations of maternally transmitted symbionts in insects: The roles of drift versus biased cotransmission and selection. Molecular Ecology, 28, 5330–5346. https://doi.org/10.1111/mec.15206

Mira A, Moran NA (2002) Estimating Population Size and Transmission Bottlenecks in Maternally Transmitted Endosymbiotic Bacteria. Microbial Ecology, 44, 137–143. https://doi.org/10.1007/s00248-002-0012-9

Vale PF, Wilson AJ, Best A, Boots M, Little TJ (2011) Epidemiological, Evolutionary, and Coevolutionary Implications of Context-Dependent Parasitism. The American Naturalist, 177, 510–521. https://doi.org/10.1086/659002

Wale N, Jones MJ, Sim DG, Read AF, King AA (2019) The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections. Proceedings of the National Academy of Sciences, 116, 22386–22392. https://doi.org/10.1073/pnas.1908147116