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11 May 2021
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Wolbachia load variation in Drosophila is more likely caused by drift than by host genetic factors

Drift rather than host or parasite control can explain within-host Wolbachia growth

Recommended by and based on reviews by Simon Fellous and 1 anonymous reviewer

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

 

Wolbachia load variation in Drosophila is more likely caused by drift than by host genetic factorsAlexis Bénard, Hélène Henri, Camille Noûs, Fabrice Vavre, Natacha Kremer <p style="text-align: justify;">Symbiosis is a continuum of long-term interactions ranging from mutualism to parasitism, according to the balance between costs and benefits for the protagonists. The density of endosymbionts is, in both cases, a ke...Evolutionary Dynamics, Genetic conflicts, Species interactionsAlison Duncan2020-12-01 16:28:14 View
14 Apr 2021
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Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host species

What makes a parasite successful? Parasitoid wasp venoms evolve rapidly in a host-specific manner

Recommended by based on reviews by Simon Fellous, alexandre leitão and 1 anonymous reviewer

Parasitoid wasps have developed different mechanisms to increase their parasitic success, usually at the expense of host survival (Fellowes and Godfray, 2000). Eggs of these insects are deposited inside the juvenile stages of their hosts, which in turn deploy several immune response strategies to eliminate or disable them (Yang et al., 2020). Drosophila melanogaster protects itself against parasitoid attacks through the production of specific elongated haemocytes called lamellocytes which form a capsule around the invading parasite (Lavine and Strand, 2002; Rizki and Rizki, 1992) and the subsequent activation of the phenol-oxidase cascade leading to the release of toxic radicals (Nappi et al., 1995). On the parasitoid side, robust responses have evolved to evade host immune defenses as for example the Drosophila-specific endoparasite Leptopilina boulardi, which releases venom during oviposition that modifies host behaviour (Varaldi et al., 2006) and inhibits encapsulation (Gueguen et al., 2011; Martinez et al., 2012).
Studies have shown that the wasp parasitic capacity is correlated to venom presence and its content (Colinet et al., 2009; Poirié et al., 2014), including that evolution of venom protein composition is driven by different levels of host susceptibility to infection (Cavigliasso et al., 2019). However, it had not been determined to this day, if and how parasitic range can affect venom protein composition and to which extent host specialization requires broad-spectrum factors or a plethora of specialized components.
These outstanding questions are now approached in a study by Cavigliasso and colleagues (Cavigliasso et al., 2021), where they perform experimental evolution of L. boulardi for 9 generations exposing it to different Drosophila host species and genetic backgrounds (two strains of D. melanogaster, D. simulans and D. yakuba). The authors tested whether the parasitic success of each selection regime was host-specific and how they influenced venom composition in parasitoids. For the first part, infection outcomes were assayed for each selection regime when cross-infecting different hosts. To get a finer measurement of the mechanisms under selection, the authors differentiated three phenotypes: overall parasitic success, encapsulation inhibition and escape from capsule. Throughout the course of experimental evolution, only encapsulation inhibition did not show an improved response upon selection on any host. Importantly, the cross-infection scenario revealed a clear specificity to the selected host for each evolved resistance.
As for venom composition, a trend of differential evolution was detected between host species, although a significant part of that was due to a larger differentiation in the D. yakuba regime, which showed a completely different directionality. Importantly, the authors could identify some of the specific proteins targeted by the several selection regimes, whether selected or counter-selected for. Interestingly, the D. yakuba regime is the only case where the key parasitoid protein LbSPNy (Colinet et al., 2009) was not counter-selected and the only regime in which the overall venom composition did not evolve towards the Ism strain, one of the two ancestral strains of L. boulardi used in the study. It is possible that these two results are correlated, since LbSPNy has been described to inhibit activation of the phenoloxidase cascade in D. yakuba and is one of the most abundant proteins in the ISy venom, making it a good target for selection (Colinet et al., 2013). The authors also discuss the possibility that this difference is related to the geographical distribution of the strains of L. boulardi, since each coincide with either D. melanogaster or D. yakuba.
This methodologically broad work by Cavigliasso and colleagues constitutes an important experimental contribution towards the understanding of how parasitoid adaptation to specific hosts is achieved at different phenotypic and mechanistic levels. It provides compelling evidence that venom composition evolves differently in response to specific parasitic ranges, particularly considering the evolutionary difference between the selective hosts. In line with this result, it is also concluded that the majority of venom proteins selected are lineage-specific, although a few broad-spectrum factors could also be detected. 
The question of whether parasitic range can affect venom composition and parasitic success is still open to more contributions. A potentially interesting long-term direction will be to use a similar setup of experimental evolution on the generalist L. heterotoma (Schlenke et al., 2007) . On a more immediate horizon, comparing the venom evolution of both L. heterotoma and L. boulardi under selection with different hosts and under cross-infection scenarios could reveal interesting patterns. The recent sequencing of the L. boulardi genome together with the vast number of studies addressing mechanisms of Drosophila resistance to parasitoid infection, will enable the thorough characterization of the genetic basis of host-parasitoid interactions and the deeper understanding of these ubiquitous and economically-relevant relationships.
 
*This recommendation text has been co-written with Tânia F. Paulo who is not a recommender of PCI Evol Biol

 

References

Cavigliasso, F., Mathé-Hubert, H., Gatti, J.-L., Colinet, D. and Poirié, M. (2021) Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host species. bioRxiv, 2020.10.24.353417, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2020.10.24.353417

Cavigliasso, F., Mathé-Hubert, H., Kremmer, L., Rebuf, C., Gatti, J.-L., Malausa, T., Colinet, D., Poiré, M. and  Léne. (2019). Rapid and Differential Evolution of the Venom Composition of a Parasitoid Wasp Depending on the Host Strain. Toxins, 11(629). https://doi.org/10.3390/toxins11110629

Colinet, D., Deleury, E., Anselme, C., Cazes, D., Poulain, J., Azema-Dossat, C., Belghazi, M., Gatti, J. L. and  Poirié, M. (2013). Extensive inter- and intraspecific venom variation in closely related parasites targeting the same host: The case of Leptopilina parasitoids of Drosophila. Insect Biochemistry and Molecular Biology, 43(7), 601–611. https://doi.org/10.1016/j.ibmb.2013.03.010

Colinet, D., Dubuffet, A., Cazes, D., Moreau, S., Drezen, J. M. and  Poirié, M. (2009). A serpin from the parasitoid wasp Leptopilina boulardi targets the Drosophila phenoloxidase cascade. Developmental and Comparative Immunology, 33(5), 681–689. https://doi.org/10.1016/j.dci.2008.11.013

Fellowes, M. D. E. and  Godfray, H. C. J. (2000). The evolutionary ecology of resistance to parasitoids by Drosophila. Heredity, 84(1), 1–8. https://doi.org/10.1046/j.1365-2540.2000.00685.x

Gueguen, G., Rajwani, R., Paddibhatla, I., Morales, J. and  Govind, S. (2011). VLPs of Leptopilina boulardi share biogenesis and overall stellate morphology with VLPs of the heterotoma clade. Virus Research, 160(1–2), 159–165. https://doi.org/10.1016/j.virusres.2011.06.005

Lavine, M. D. and  Strand, M. R. (2002). Insect hemocytes and their role in immunity. Insect Biochemistry and Molecular Biology, 32(10), 1295–1309. https://doi.org/10.1016/S0965-1748(02)00092-9

Martinez, J., Duplouy, A., Woolfit, M., Vavre, F., O’Neill, S. L. and  Varaldi, J. (2012). Influence of the virus LbFV and of Wolbachia in a host-parasitoid interaction. PloS One, 7(4), e35081. https://doi.org/10.1371/journal.pone.0035081

Nappi, A. J., Vass, E., Frey, F. and  Carton, Y. (1995). Superoxide anion generation in Drosophila during melanotic encapsulation of parasites. European Journal of Cell Biology, 68(4), 450–456.

Poirié, M., Colinet, D. and  Gatti, J. L. (2014). Insights into function and evolution of parasitoid wasp venoms. Current Opinion in Insect Science, 6, 52–60. https://doi.org/10.1016/j.cois.2014.10.004

Rizki, T. M. and  Rizki, R. M. (1992). Lamellocyte differentiation in Drosophila larvae parasitized by Leptopilina. Developmental and Comparative Immunology, 16(2–3), 103–110. https://doi.org/10.1016/0145-305X(92)90011-Z

Schlenke, T. A., Morales, J., Govind, S. and  Clark, A. G. (2007). Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster. PLoS Pathogens, 3(10), 1486–1501. https://doi.org/10.1371/journal.ppat.0030158

Varaldi, J., Petit, S., Boulétreau, M. and  Fleury, F. (2006). The virus infecting the parasitoid Leptopilina boulardi exerts a specific action on superparasitism behaviour. Parasitology, 132(Pt 6), 747–756. https://doi.org/10.1017/S0031182006009930

Yang, L., Qiu, L., Fang, Q., Stanley, D. W. and  Gong‐Yin, Y. (2020). Cellular and humoral immune interactions between Drosophila and its parasitoids. Insect Science. https://doi.org/10.1111/1744-7917.12863

 

Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host speciesFanny Cavigliasso, Hugo Mathé-Hubert, Jean-Luc Gatti, Dominique Colinet, Marylène Poirié<p>Female endoparasitoid wasps usually inject venom into hosts to suppress their immune response and ensure offspring development. However, the parasitoid’s ability to evolve towards increased success on a given host simultaneously with the evolut...Experimental Evolution, Species interactionsÉlio Sucena2020-10-26 15:00:55 View
06 Apr 2021
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How robust are cross-population signatures of polygenic adaptation in humans?

Be careful when studying selection based on polygenic score overdispersion

Recommended by ORCID_LOGO based on reviews by Lawrence Uricchio, Mashaal Sohail, Barbara Bitarello and 1 anonymous reviewer

The advent of genome-wide association studies (GWAS) has been a great promise for our understanding of the connection between genotype and phenotype. Today, the NHGRI-EBI GWAS catalog contains 251,401 associations from 4,961 studies (1). This wealth of studies has also generated interest to use the summary statistics beyond the few top hits in order to make predictions for individuals without known phenotype, e.g. to predict polygenic risk scores or to study polygenic selection by comparing different groups. For instance, polygenic selection acting on the most studied polygenic trait, height, has been subject to multiple studies during the past decade (e.g. 2–6). They detected north-south gradients in Europe which were consistent with expectations. However, their GWAS summary statistics were based on the GIANT consortium data set, a meta-analysis of GWAS conducted in different European cohorts (7,8). The availability of large data sets with less stratification such as the UK Biobank (9) has led to a re-evaluation of those results. The nature of the GIANT consortium data set was realized to represent a potential problem for studies of polygenic adaptation which led several of the authors of the original articles to caution against the interpretations of polygenic selection on height (10,11). This was a great example on how the scientific community assessed their own earlier results in a critical way as more data became available. At the same time it left the question whether there is detectable polygenic selection separating populations more open than ever.

Generally, recent years have seen several articles critically assessing the portability of GWAS results and risk score predictions to other populations (12–14). Refoyo-Martínez et al. (15) are now presenting a systematic assessment on the robustness of cross-population signatures of polygenic adaptation in humans. They compiled GWAS results for complex traits which have been studied in more than one cohort and then use allele frequencies from the 1000 Genomes Project data (16) set to detect signals of polygenic score overdispersion. As the source for the allele frequencies is kept the same across all tests, differences between the signals must be caused by the underlying GWAS. The results are concerning as the level of overdispersion largely depends on the choice of GWAS cohort. Cohorts with homogenous ancestries show little to no overdispersion compared to cohorts of mixed ancestries such as meta-analyses. It appears that the meta-analyses fail to fully account for stratification in their data sets.

The authors based most of their analyses on the heavily studied trait height. Additionally, they use educational attainment (measured as the number of school years of an individual) as an example. This choice was due to the potential over- or misinterpretation of results by the media, the general public and by far right hate groups. Such traits are potentially confounded by unaccounted cultural and socio-economic factors. Showing that previous results about polygenic selection on educational attainment are not robust is an important result that needs to be communicated well. This forms a great example for everyone working in human genomics. We need to be aware that our results can sometimes be misinterpreted. And we need to make an effort to write our papers and communicate our results in a way that is honest about the limitations of our research and that prevents the misuse of our results by hate groups.

This article represents an important contribution to the field. It is cruicial to be aware of potential methodological biases and technical artifacts. Future studies of polygenic adaptation need to be cautious with their interpretations of polygenic score overdispersion. A recommendation would be to use GWAS results obtained in homogenous cohorts. But even if different biobank-scale cohorts of homogeneous ancestry are employed, there will always be some remaining risk of unaccounted stratification. These conclusions may seem sobering but they are part of the scientific process. We need additional controls and new, different methods than polygenic score overdispersion for assessing polygenic selection. Last year also saw the presentation of a novel approach using sequence data and GWAS summary statistics to detect directional selection on a polygenic trait (17). This new method appears to be robust to bias stemming from stratification in the GWAS cohort as well as other confounding factors. Such new developments show light at the end of the tunnel for the use of GWAS summary statistics in the study of polygenic adaptation.

References

1. Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Research. 2019 Jan 8;47(D1):D1005–12. doi: https://doi.org/10.1093/nar/gky1120

2. Turchin MC, Chiang CW, Palmer CD, Sankararaman S, Reich D, Hirschhorn JN. Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Nature Genetics. 2012 Sep;44(9):1015–9. doi: https://doi.org/10.1038/ng.2368

3. Berg JJ, Coop G. A Population Genetic Signal of Polygenic Adaptation. PLOS Genetics. 2014 Aug 7;10(8):e1004412. doi: https://doi.org/10.1371/journal.pgen.1004412

4. Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, et al. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 2015 Nov;47(11):1357–62. doi: https://doi.org/10.1038/ng.3401

5. Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature. 2015 Dec;528(7583):499–503. doi: https://doi.org/10.1038/nature16152

6. Racimo F, Berg JJ, Pickrell JK. Detecting polygenic adaptation in admixture graphs. Genetics. 2018. Arp;208(4):1565–1584. doi: https://doi.org/10.1534/genetics.117.300489

7. Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 2010 Oct;467(7317):832–8. doi: https://doi.org/10.1038/nature09410

8. Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet. 2014 Nov;46(11):1173–86. doi: https://doi.org/10.1038/ng.3097

9. Bycroft C, Freeman C, Petkova D, Band G, Elliott LT, Sharp K, et al. The UK Biobank resource with deep phenotyping and genomic data. Nature. 2018 Oct;562(7726):203–9. doi: https://doi.org/10.1038/s41586-018-0579-z

10. Berg JJ, Harpak A, Sinnott-Armstrong N, Joergensen AM, Mostafavi H, Field Y, et al. Reduced signal for polygenic adaptation of height in UK Biobank. eLife. 2019 Mar 21;8:e39725. doi: https://doi.org/10.7554/eLife.39725

11. Sohail M, Maier RM, Ganna A, Bloemendal A, Martin AR, Turchin MC, et al. Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies. eLife. 2019 Mar 21;8:e39702. doi: https://doi.org/10.7554/eLife.39702

12. Martin AR, Kanai M, Kamatani Y, Okada Y, Neale BM, Daly MJ. Clinical use of current polygenic risk scores may exacerbate health disparities. Nature Genetics. 2019 Apr;51(4):584–91. doi: https://doi.org/10.1038/s41588-019-0379-x

13. Bitarello BD, Mathieson I. Polygenic Scores for Height in Admixed Populations. G3: Genes, Genomes, Genetics. 2020 Nov 1;10(11):4027–36. doi: https://doi.org/10.1534/g3.120.401658

14. Uricchio LH, Kitano HC, Gusev A, Zaitlen NA. An evolutionary compass for detecting signals of polygenic selection and mutational bias. Evolution Letters. 2019;3(1):69–79. doi: https://doi.org/10.1002/evl3.97

15. Refoyo-Martínez A, Liu S, Jørgensen AM, Jin X, Albrechtsen A, Martin AR, Racimo F. How robust are cross-population signatures of polygenic adaptation in humans? bioRxiv, 2021, 2020.07.13.200030, version 5 peer-reviewed and recommended by Peer community in Evolutionary Biology. doi: https://doi.org/10.1101/2020.07.13.200030

16. Auton A, Abecasis GR, Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, et al. A global reference for human genetic variation. Nature. 2015 Sep 30;526(7571):68–74. doi: https://doi.org/10.1038/nature15393

17. Stern AJ, Speidel L, Zaitlen NA, Nielsen R. Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies. bioRxiv. 2020 May 8;2020.05.07.083402. doi: https://doi.org/10.1101/2020.05.07.083402

How robust are cross-population signatures of polygenic adaptation in humans?Alba Refoyo-Martínez, Siyang Liu, Anja Moltke Jørgensen, Xin Jin, Anders Albrechtsen, Alicia R. Martin, Fernando Racimo<p>Over the past decade, summary statistics from genome-wide association studies (GWASs) have been used to detect and quantify polygenic adaptation in humans. Several studies have reported signatures of natural selection at sets of SNPs associated...Bioinformatics & Computational Biology, Genetic conflicts, Human Evolution, Population Genetics / GenomicsTorsten Günther2020-08-14 15:06:54 View
04 Mar 2021
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Simulation of bacterial populations with SLiM

Simulating bacterial evolution forward-in-time

Recommended by based on reviews by 3 anonymous reviewers

Jean Cury and colleagues (2021) have developed a protocol to simulate bacterial evolution in SLiM. In contrast to existing methods that depend on the coalescent, SLiM simulates evolution forward in time. SLiM has, up to now, mostly been used to simulate the evolution of eukaryotes (Haller and Messer 2019), but has been adapted here to simulate evolution in bacteria. Forward-in-time simulations are usually computationally very costly. To circumvent this issue, bacterial population sizes are scaled down. One would now expect results to become inaccurate, however, Cury et al. show that scaled-down forwards simulations provide very accurate results (similar to those provided by coalescent simulators) that are consistent with theoretical expectations. Simulations were analyzed and compared to existing methods in simple and slightly more complex scenarios where recombination affects evolution. In all scenarios, simulation results from coalescent methods (fastSimBac (De Maio and Wilson 2017), ms (Hudson 2002)) and scaled-down forwards simulations were very similar, which is very good news indeed.

A biologist not aware of the complexities of forwards, backwards simulations and the coalescent, might now naïvely ask why another simulation method is needed if existing methods perform just as well. To address this question the manuscript closes with a very neat example of what exactly is possible with forwards simulations that cannot be achieved using existing methods. The situation modeled is the growth and evolution of a set of 50 bacteria that are randomly distributed on a petri dish. One side of the petri dish is covered in an antibiotic the other is antibiotic-free. Over time, the bacteria grow and acquire antibiotic resistance mutations until the entire artificial petri dish is covered with a bacterial lawn. This simulation demonstrates that it is possible to simulate extremely complex (e.g. real world) scenarios to, for example, assess whether certain phenomena are expected with our current understanding of bacterial evolution, or whether there are additional forces that need to be taken into account. Hence, forwards simulators could significantly help us to understand what current models can and cannot explain in evolutionary biology.  

 

References  

Cury J, Haller BC, Achaz G, Jay F (2021) Simulation of bacterial populations with SLiM. bioRxiv, 2020.09.28.316869, version 5 peer-reviewed and recommended by Peer community in Evolutionary Biology.  https://doi.org/10.1101/2020.09.28.316869

De Maio N, Wilson DJ (2017) The Bacterial Sequential Markov Coalescent. Genetics, 206, 333–343. https://doi.org/10.1534/genetics.116.198796

Haller BC, Messer PW (2019) SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model. Molecular Biology and Evolution, 36, 632–637. https://doi.org/10.1093/molbev/msy228

Hudson RR (2002) Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics, 18, 337–338. https://doi.org/10.1093/bioinformatics/18.2.337

Simulation of bacterial populations with SLiMJean Cury, Benjamin C. Haller, Guillaume Achaz, and Flora Jay<p>Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate...Bioinformatics & Computational Biology, Population Genetics / GenomicsFrederic Bertels2020-10-02 19:03:42 View
01 Mar 2021
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Social Conflicts in Dictyostelium discoideum : A Matter of Scales

The cell-level perspective in social conflicts in Dictyostelium discoideum

Recommended by Jeremy Van Cleve based on reviews by Peter Conlin and ?

The social amoeba Dictyostelium discoideum is an important model system for the study of cooperation and multicellularity as is has both unicellular and aggregative life phases. In the aggregative phase, which typically occurs when nutrients are limiting, individual cells eventually gather together to form a fruiting bodies whose spores may be dispersed to another, better, location and whose stalk cells, which support the spores, die. This extreme form of cooperation has been the focus of numerous studies that have revealed the importance genetic relatedness and kin selection (Hamilton 1964; Lehmann and Rousset 2014) in explaining the maintenance of this cooperative collective behavior (Strassmann et al. 2000; Kuzdzal-Fick et al. 2011; Strassmann and Queller 2011). However, much remains unknown with respect to how the interactions between individual cells, their neighbors, and their environment produce cooperative behavior at the scale of whole groups or collectives. In this preprint, Forget et al. (2021) describe how the D. discoideum system is crucial in this respect because it allows these cellular-level interactions to be studied in a systematic and tractable manner.
Spore bias, which is the tendency of a particular genotype or strain to disproportionately migrate to the spore instead of the stalk, is often used to define which strains are "cheaters" (positive spore bias) and which are "cooperative" (negative spore bias). Forget et al. (2021) note that spore bias depends on a number of stochastic factors including external drivers such as variation in environmental (or nutrient) quality and internal drivers like cell-cycle phase at the time of starvation. Spore bias is also affected by the social environment where the fraction of cheater strains in a spore may be limited by the ability of the remaining stalk cells to support the spore. The social environment can also affect cells through their differential responsiveness to the chemical factors that induce differentiation into stalk cells; responsiveness is partly a function of nutrient quality (Thompson and Kay 2000), which in turn can be a function of cell density. Thus, Forget et al. (2021) highlight a number of mechanisms that could generate frequency-dependent selection that would lead to the stable maintenance of multiple strains with different spore biases; in other words, both cheater and cooperative strains might stably coexist due to these cellular-level interactions.
The cellular-level interactions that Forget et al. (2021) highlight are particularly important because they pose a challenge evolutionary theory: some evolutionary models of social and collective behavior neglect or simplify these interactions. For example, Forget et al. (2021) note that the developmental, behavior, and environmental timescales relevant for Dictyostelium fruiting body formation all overlap. Evolutionary analyses often assume some of these timescales, for example developmental and behavior, are separate in order to simplify the analysis of any interactions. Thus, new theoretical work that allows these timescales to overlap may shed light on how cellular-level interactions can produce environmental, physiological, and behavioral feedbacks that drive the evolution of cooperation and other collective behaviors.

References

Forget, M., Adiba, S. and De Monte, S.(2021) Social conflicts in *Dictyostelium discoideum *: a matter of scales. HAL, hal-03088868, ver. 2 peer-reviewed and recommended by PCI Evolutionary Biology. https://hal.archives-ouvertes.fr/hal-03088868/

Hamilton, W. D. (1964). The genetical evolution of social behaviour. II. Journal of theoretical biology, 7(1), 17-52. doi: https://doi.org/10.1016/0022-5193(64)90039-6

Kuzdzal-Fick, J. J., Fox, S. A., Strassmann, J. E., and Queller, D. C. (2011). High relatedness is necessary and sufficient to maintain multicellularity in Dictyostelium. Science, 334(6062), 1548-1551. doi: https://doi.org/10.1126/science.1213272

Lehmann, L., and Rousset, F. (2014). The genetical theory of social behaviour. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1642), 20130357. doi: https://doi.org/10.1098/rstb.2013.0357

Strassmann, J. E., and Queller, D. C. (2011). Evolution of cooperation and control of cheating in a social microbe. Proceedings of the National Academy of Sciences, 108(Supplement 2), 10855-10862. doi: https://doi.org/10.1073/pnas.1102451108

Strassmann, J. E., Zhu, Y., & Queller, D. C. (2000). Altruism and social cheating in the social amoeba Dictyostelium discoideum. Nature, 408(6815), 965-967. doi: https://doi.org/10.1038/35050087

Thompson, C. R., & Kay, R. R. (2000). Cell-fate choice in Dictyostelium: intrinsic biases modulate sensitivity to DIF signaling. Developmental biology, 227(1), 56-64. doi: https://doi.org/10.1006/dbio.2000.9877

Social Conflicts in Dictyostelium discoideum : A Matter of Scales Forget, Mathieu; Adiba, Sandrine; De Monte, Silvia<p>The 'social amoeba' Dictyostelium discoideum, where aggregation of genetically heterogeneous cells produces functional collective structures, epitomizes social conflicts associated with multicellular organization. 'Cheater' populations that hav...Behavior & Social Evolution, Evolutionary Dynamics, Evolutionary Theory, Experimental EvolutionJeremy Van Cleve2020-08-28 10:37:21 View
25 Feb 2021
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Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig

Assessing the role of host-symbiont interactions in maternal care behaviour

Recommended by ORCID_LOGO based on reviews by Nadia Aubin-Horth, Gabrielle Davidson and 1 anonymous reviewer

The role of microbial symbionts in governing social traits of their hosts is an exciting and developing research area. Just like symbionts influence host reproductive behaviour and can cause mating incompatibilities to promote symbiont transmission through host populations (Engelstadter and Hurst 2009; Correa and Ballard 2016; Johnson and Foster 2018) (see also discussion on conflict resolution in Johnsen and Foster 2018), microbial symbionts could enhance transmission by promoting the social behaviour of their hosts (Ezenwa et al. 2012; Lewin-Epstein et al. 2017; Gurevich et al. 2020). Here I apply the term ‘symbiosis’ in the broad sense, following De Bary 1879 as “the living together of two differently named organisms“ independent of effects on the organisms involved (De Bary 1879), i.e. the biological interaction between the host and its symbionts may include mutualism, parasitism and commensalism.
So far, we have relative few studies that explore the role of symbionts in promoting social behaviours such as parental care. Clearly, disentangling cause and effect when assessing the functional significance of symbiotic relationships in general is extremely challenging, and perhaps even more caution is needed when assessing the role of symbionts in the evolution of parental care, given the high fitness benefits to the offspring of receiving care. An interesting study on the symbiotic relationship between termites and their eukaryotic gut symbionts proposes a role of gut flagellates in the origin of subsocial behaviour (extended offspring care) in the termites through proctodeal trophallaxis (i.e. anus-to-mouth feeding), driven by mutualistic beneficial interactions (Nalepa 2020). Van Meyel et al. (2021) hypothesized a role of gut symbionts in promoting maternal care behaviour in the European earwig, and set out to test this idea in a carefully executed experimental study. They used a broad-spectrum antibiotic treatment to alter gut microbiota in mothers and examined its effect on maternal care provisioning. While the antibiotic treatment altered the gut microbiome, no effect on pre- or post-hatching maternal care was detected. The authors also investigated a broad range of physiological and reproductive traits measured over a major part of a female’s lifetime, and detected no effect of microbiome alteration on these traits. The study therefore does not provide evidence for a direct role of the gut microbiome in shaping offspring care in this population of European earwigs.
Within populations, earwigs show inter-individual variation in the expression of maternal care (Meunier et al. 2012; Ratz et al. 2016), and there is evidence that genetic and environmental factors contribute to this this variation (Meunier and Kolliker 2012; Kramer et al. 2017). The study by Van Meyel et al. (2021) is the first to analyse microbiome composition of the European earwig, and they study host-symbiont associations in a single population. A next step could be to explore among population variation in the gut microbiome, to achieve a better understanding on host-microbiome variation and dynamics in wild populations. Depending on the nature of host-symbiont associations across populations, new perspectives on their functional significance may arise (Hird 2017; Johnson and Foster 2018). It is therefore too early to conclusively confirm or reject the role of microbial symbionts in the expression of parental care in this system.

References

Correa, C. C., and Ballard, J. W. O. (2016). Wolbachia associations with insects: winning or losing against a master manipulator. Frontiers in Ecology and Evolution, 3, 153. doi: https://doi.org/10.3389/fevo.2015.00153

De Bary, A. (1879). Die Erscheinung der Symbiose. Verlag von Karl J. Trubner, Strassburg.

Engelstädter, J., and Hurst, G. D. (2009). The ecology and evolution of microbes that manipulate host reproduction. Annual Review of Ecology, Evolution, and Systematics, 40, 127-149. doi: https://doi.org/10.1146/annurev.ecolsys.110308.120206

Ezenwa, V. O., Gerardo, N. M., Inouye, D. W., Medina, M., and Xavier, J. B. (2012). Animal behavior and the microbiome. Science, 338(6104), 198-199. doi: https://doi.org/10.1126/science.1227412

Gurevich, Y., Lewin-Epstein, O., and Hadany, L. (2020). The evolution of paternal care: a role for microbes?. Philosophical Transactions of the Royal Society B, 375(1808), 20190599. doi: https://doi.org/10.1098/rstb.2019.0599

Hird, S. M. (2017). Evolutionary biology needs wild microbiomes. Frontiers in microbiology, 8, 725. doi: https://doi.org/10.3389/fmicb.2017.00725

Johnson, K. V. A., and Foster, K. R. (2018). Why does the microbiome affect behaviour?. Nature reviews microbiology, 16(10), 647-655. doi: https://doi.org/10.1038/s41579-018-0014-3

Kramer et al. (2017). When earwig mothers do not care to share: parent–offspring competition and the evolution of family life. Functional Ecology, 31(11), 2098-2107. doi: https://doi.org/10.1111/1365-2435.12915

Lewin-Epstein, O., Aharonov, R., and Hadany, L. (2017). Microbes can help explain the evolution of host altruism. Nature communications, 8(1), 1-7. doi: https://doi.org/10.1038/ncomms14040

Meunier, J., and Kölliker, M. (2012). Parental antagonism and parent–offspring co-adaptation interact to shape family life. Proceedings of the Royal Society B: Biological Sciences, 279(1744), 3981-3988. doi: https://doi.org/10.1098/rspb.2012.1416

Meunier, J., Wong, J. W., Gómez, Y., Kuttler, S., Röllin, L., Stucki, D., and Kölliker, M. (2012). One clutch or two clutches? Fitness correlates of coexisting alternative female life-histories in the European earwig. Evolutionary Ecology, 26(3), 669-682. doi: https://doi.org/10.1007/s10682-011-9510-x

Nalepa, C. A. (2020). Origin of mutualism between termites and flagellated gut protists: transition from horizontal to vertical transmission. Frontiers in Ecology and Evolution, 8, 14. doi: https://doi.org/10.3389/fevo.2020.00014

Ratz, T., Kramer, J., Veuille, M., and Meunier, J. (2016). The population determines whether and how life-history traits vary between reproductive events in an insect with maternal care. Oecologia, 182(2), 443-452. doi: https://doi.org/10.1007/s00442-016-3685-3

Van Meyel, S., Devers, S., Dupont, S., Dedeine, F. and Meunier, J. (2021) Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwig. bioRxiv, 2020.10.08.331363. ver. 5 peer-reviewed and recommended by PCI Evol Biol. https://doi.org/10.1101/2020.10.08.331363

Alteration of gut microbiota with a broad-spectrum antibiotic does not impair maternal care in the European earwigSophie Van Meyel, Séverine Devers, Simon Dupont, Franck Dedeine and Joël Meunier<p>The microbes residing within the gut of an animal host often increase their own fitness by modifying their host’s physiological, reproductive, and behavioural functions. Whereas recent studies suggest that they may also shape host sociality and...Behavior & Social Evolution, Evolutionary Ecology, Experimental Evolution, Life History, Species interactionsTrine Bilde2020-10-09 14:07:47 View
05 Feb 2021
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Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees

Multi-gene and lineage comparative assessment of the strength of selection in Hymenoptera

Recommended by based on reviews by Michael Lattorff and 1 anonymous reviewer

Genetic variation is the raw material for selection to act upon and the amount of genetic variation present within a population is a pivotal determinant of a population’s evolutionary potential. A large effective population size, i.e., the ideal number of individuals experiencing the same amount of genetic drift and inbreeding as an actual population, Ne (Wright 1931, Crow 1954), thus increases the probability of long-term survival of a population. However, natural populations, as opposed to theoretical ones, rarely adhere to the requirements of an ideal panmictic population (Sjödin et al. 2005). A range of circumstances can reduce Ne, including the structuring of populations (through space and time, as well as age and developmental stages) and inbreeding (Charlesworth 2009). In mammals, species with a larger body mass (as a proxy for lower Ne) were found to have a higher rate of nonsynonymous nucleotide substitutions (that alter the amino acid sequence of a protein), as well as radical amino acid substitutions (altering the physicochemical properties of a protein) (Popadin et al. 2007). In general, low effective population sizes increase the chance of mutation accumulation and drift, while reducing the strength of selection (Sjödin et al. 2005).
In this paper, Weyna and Romiguier (2021) set out to test if parasitism, body size, geographic range, and/or eusociality affect the strength of selection in Hymenoptera. Hymenoptera include the bees, wasps and ants and is an extraordinarily diverse order within the insects. It was recently estimated that Hymenoptera is the most speciose order of the animal kingdom (Forbes et al. 2018). Hymenoptera are further characterized by an impressive radiation of parasitic species, mainly parasitoids, that feed in or on a single host individual to complete their own development (Godfray 1994). All hymenopterans share the same sex determination system: haplo-diploidy, where unfertilized eggs are haploid males and fertilized eggs are diploid females. Compared to other animals, Hymenoptera further contain an impressive number of clades that evolved eusociality (Rehan and Toth 2015), in which societies show a clear division of labor for reproduction (i.e., castes) and cooperative brood care. Hymenopterans thus represent a diverse and interesting group of insects to investigate potential factors affecting strength of selection and Ne.
Using a previously published phylogenomic dataset containing 3256 genes and 169 hymenopteran species (Peters et al. 2017), Weyna and Romiguier (2021) estimated mean genomic dN/dS ratios (nonsynonymous to synonymous substitution rates) for each species and compared these values between parasitic and non-parasitic species, eusocial and solitary species, and in relation to body size, parasitoid-specific traits and geographic range, thought to affect the effective population size and strength of selection. The use of a large number of species, as well as several distinct traits is a clear asset of this study. The authors found no effect of body size, geographic range or parasitism (including a range of parasitoid-specific traits). There was an effect, however, of eusociality where dN/dS increased in three out of four eusocial lineages. Future studies including more independent evolutionary transitions to eusociality can lend further support that eusocial species indeed reduces the efficiency of selection. The most intriguing result was that for solitary and social bees, with high dN/dS ratios and a strong signature of relaxed selection (i.e., the elimination or reduction of a source of selection (Lahti et al. 2009). The authors suggest that the pollen-collecting behaviors of these species can constrain Ne, as pollen availability varies at both a spatial and temporal scale, requiring a large investment in foraging that may in turn limit reproductive output. It would be interesting to see if other pollen feeders, such as certain beetles, flies, butterflies and moths, as well as mites and spiders, experience relaxed selection as a consequence of the trade-off between energy investment in pollen foraging versus fecundity.

References

Charlesworth, B. (2009). Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics, 10(3), 195-205. doi: https://doi.org/10.1038/nrg2526
Crow, J. F. (1954) Statistics and Mathematics in Biology (eds Kempthorne, O., Bancroft, T. A., Gowen, J. W. & Lush, J. L.) 543–556 (Iowa State Univ. Press, Ames, Iowa)
Forbes, A. A., Bagley, R. K., Beer, M. A., Hippee, A. C., and Widmayer, H. A. (2018). Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order. BMC ecology, 18(1), 1-11. doi: https://doi.org/10.1186/s12898-018-0176-x
Godfray, H. C. J. (1994) Parasitoids: Behavioral and Evolutionary Ecology. Vol. 67, Princeton University Press, 1994. doi: https://doi.org/10.2307/j.ctvs32rmp
Lahti et al. (2009). Relaxed selection in the wild. Trends in ecology & evolution, 24(9), 487-496. doi: https://doi.org/10.1016/j.tree.2009.03.010
Peters et al. (2017). Evolutionary history of the Hymenoptera. Current Biology, 27(7), 1013-1018. doi: https://doi.org/10.1016/j.cub.2017.01.027
Popadin, K., Polishchuk, L. V., Mamirova, L., Knorre, D., and Gunbin, K. (2007). Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proceedings of the National Academy of Sciences, 104(33), 13390-13395. doi: https://doi.org/10.1073/pnas.0701256104
Rehan, S. M., and Toth, A. L. (2015). Climbing the social ladder: the molecular evolution of sociality. Trends in ecology & evolution, 30(7), 426-433. doi: https://doi.org/10.1016/j.tree.2015.05.004
Sjödin, P., Kaj, I., Krone, S., Lascoux, M., and Nordborg, M. (2005). On the meaning and existence of an effective population size. Genetics, 169(2), 1061-1070. doi: https://doi.org/10.1534/genetics.104.026799
Weyna, A., and Romiguier, J. (2021) Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees. bioRxiv, 2020.04.14.038893, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: https://doi.org/10.1101/2020.04.14.038893
Wright, S. (1931). Evolution in Mendelian populations. Genetics, 16(2), 97-159.

Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating beesArthur Weyna, Jonathan Romiguier<p>With one of the highest number of parasitic, eusocial and pollinator species among all insect orders, Hymenoptera features a great diversity of lifestyles. At the population genetic level, such life-history strategies are expected to decrease e...Behavior & Social Evolution, Genome Evolution, Life History, Molecular Evolution, Population Genetics / GenomicsBertanne Visser2020-04-21 17:30:57 View
18 Jan 2021
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Trait plasticity and covariance along a continuous soil moisture gradient

Another step towards grasping the complexity of the environmental response of traits

Recommended by based on reviews by 2 anonymous reviewers

One can only hope that one day, we will be able to evaluate how the ecological complexity surrounding natural populations affects their ability to adapt. This is more like a long term quest than a simple scientific aim. Many steps are heading in the right direction. This paper by Monroe and colleagues (2021) is one of them.
Many ecological and genetic mechanisms shape the evolutionary potential of phenotypic trait variation and many of them involve environmental heterogeneity (Pujol et al 2018). To date, we cannot look into these ecological and genetic mechanisms without oversimplifying their effects. We often look into trait variation one trait at a time albeit the variation of multiple phenotypic traits is often linked at the genetic or environmental level. As a consequence, we put our conclusions at risk by not accounting for the reciprocal impacts of trait changes upon each other (Teplitsky et al 2014). We also usually restrict the study of a continuous gradient of environmental conditions to a few conditions because it would otherwise be impossible to model its environmental effect. As a consequence, we miss the full picture of the continuous often nonlinear phenotypic plastic response. Whether the trait undergo threshold effect changes thereby remains obscured to us. Collectively, these issues impede our ability to understand how selection shapes the ecological strategy of organisms under variable environments.
In this paper, Monroe and colleagues (2021) propose an original approach that raised to these two challenges. They analysed phenotypic plastic changes in response to a continuous environment in a multidimensional trait space, namely the response of Brachypodium plant developmental and physiological traits to a continuous gradient of soil moisture. They used dry down experimental treatments to produce the continuous soil moisture gradient and compared the plant capacity to use water between annual B. distachyon and perennial B. sylvaticum. Their results revealed the best mathematical functions that model the nonlinear curvature of the continuous plastic response of Brachypodium plants. This work reinforces our view that nonlinear plastic responses can result in greater or lesser trait values at any stage of the environmental gradient that were unexpected on the basis of linear predictors (Gienapp and Brommer 2014). Their findings also imply that different threshold responses characterize different genotypes. These could otherwise have been missed by a classical approach. By shedding light on unforeseen interactions between traits that make their correlation vary along the nonlinear response, they were able to describe more accurately Brachypodium ecological strategies and the changes in evolutionary constraints along the soil moisture gradient.
Their empirical approach allows to test what environmental conditions maximises the opportunity for selection to shape trait variation. For example, it revealed unforeseen divergence in potentially adaptive mechanisms or life history strategies – and not just trait values – between annual and perennial species of Brachypodium. Behind every environmental variation of the constraints to the future evolutionary change of multiple traits, we can expect that the evolutionary history of the populations shaped their trait genetic correlations. Investigating the nonlinear signature of adaptive evolution across continuous environments will get us into uncharted territory.
Our ability to predict the adaptive potential of species is limited. With their approach of continuous environmental gradients beyond linearity, Monroe and collaborators (2021) improve our understanding of plant phenotypic responses and open a brand new range of exciting developments. As they mention: "the opportunity for scaling up" their approach is big. To illustrate this prospect, I can easily think of an example: the quantitative genetic random regression model. This model allows to use any degree of genetic relatedness in a wild population to estimate the genetic variation of phenotypic plastic reaction norms (Nussey et al 2007, Pujol and Galaud 2013). However, in this approach, only a few modalities of the environmental gradient are used to model nonlinear phenotypic plastic responses. From there, it is rather intuitive. Combining the best of these two approaches (continuity of genetic relatedness in the wild & continuity of environmental gradient in experiments) could open ground breaking new perspectives in research.

References

Gienapp P. & J.E. Brommer. 2014. Evolutionary dynamics in response to climate change. In: Charmentier A, Garant D, Kruuk LEB, editors. Quantitative genetics in the wild. Oxford: Oxford University Press, Oxford. pp. 254–273. doi: https://doi.org/10.1093/acprof:oso/9780199674237.003.0015
Monroe, J. G., Cai, H., and Des Marais, D. L. (2020). Trait plasticity and covariance along a continuous soil moisture gradient. bioRxiv, 2020.02.17.952853, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: https://doi.org/10.1101/2020.02.17.952853
Pujol et al. (2018). The missing response to selection in the wild. Trends in ecology & evolution, 33(5), 337-346. doi: https://doi.org/10.1016/j.tree.2018.02.007
Pujol, B., and Galaud, J. P. (2013). A practical guide to quantifying the effect of genes underlying adaptation in a mixed genomics and evolutionary ecology approach. Botany Letters, 160(3-4), 197-204. doi: https://doi.org/10.1080/12538078.2013.799045
Nussey, D. H., Wilson, A. J., and Brommer, J. E. (2007). The evolutionary ecology of individual phenotypic plasticity in wild populations. Journal of evolutionary biology, 20(3), 831-844. doi: https://doi.org/10.1111/j.1420-9101.2007.01300.x
Teplitsky et al. (2014). Assessing multivariate constraints to evolution across ten long-term avian studies. PLoS One, 9(3), e90444. doi: https://doi.org/10.1371/journal.pone.0090444

Trait plasticity and covariance along a continuous soil moisture gradientJ Grey Monroe, Haoran Cai, David L Des Marais<p>Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because it is primarily informed by experiments considering soil moisture variabilit...Phenotypic PlasticityBenoit Pujol2020-02-20 16:34:40 View
16 Dec 2020
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Shifts from pulled to pushed range expansions caused by reduction of landscape connectivity

The push and pull between theory and data in understanding the dynamics of invasion

Recommended by based on reviews by Laura Naslund and 2 anonymous reviewers

Exciting times are afoot for those of us interested in the ecology and evolution of invasive populations. Recent years have seen evolutionary process woven firmly into our understanding of invasions (Miller et al. 2020). This integration has inspired a welter of empirical and theoretical work. We have moved from field observations and verbal models to replicate experiments and sophisticated mathematical models. Progress has been rapid, and we have seen science at its best; an intimate discussion between theory and data.
An area currently under very active development is our understanding of pushed invasions. Here a population spreads through space driven, not by dispersal and growth originating at the leading tip of the invasion, but by dispersal and growth originating deeper in the bulk of the population. These pushed invasions may be quite common – they result when per capita growth and dispersal rates are higher in the bulk of the wave than at the leading tip. They result from a range of well-known phenomena, including Allee effects and density-dependent dispersal (Gandhi et al. 2016; Bîrzu et al. 2019). Pushed invasions travel faster than we would expect given growth and dispersal rates on the leading tip, and they lose genetic diversity more slowly than classical pulled invasions (Roques et al. 2012; Haond et al. 2018; Bîrzu et al. 2019).
Well… in theory, anyway. The theory on pushed waves has momentarily streaked ahead of the empirical work, because empirical systems for studying pushed invasions are rare (though see Gandhi et al. 2016; Gandhi, Korolev, and Gore 2019). In this paper, Dahirel and colleagues (2020) make the argument that we may be able to generate pushed invasions in laboratory systems simply by reducing the connectedness of our experimental landscapes. If true, we might have a simple tool for turning many of our established experimental systems into systems for studying pushed dynamics.
It’s a nice idea, and the paper goes to careful lengths to explore the possibility in their lab system (a parasitoid wasp, Trichogramma). They run experiments on replicate wasp populations comparing strongly- v poorly-connected arrays, and estimate the resulting invasion speeds and rate of diversity loss. They also build a simulation model of the system, allowing them to explore in-silico a range of possible processes underlying their results.
As well as developing these parallel systems, Dahirel and colleagues (2020) go to careful lengths to develop statistical analyses that allow inference on key parameters, and they apply these analyses to both the experimental and simulation data. They have been motivated to apply methods that might be used in both laboratory and field settings to help classify invasions.
Ultimately, they found reasonable evidence that their poorly-connected habitat did induce a pushed dynamic. Their poorly connected invasions travelled faster than they should have if they were pulled, they lost diversity more slowly than the highly connected habitat, and replicates with a higher carrying capacity tended to have higher invasion speeds. All in line with expectations of a pushed dynamic. Interestingly, however, their simulation results suggest that they probably got this perfect result for unexpected reasons. The strong hint is that their poorly-connected habitat induced density dependent dispersal in the wasps. Without this effect, their simulations suggest they should have seen diversity decreasing much more rapidly than it did.
There is a nuanced, thoughtful, and carefully argued discussion about all this in the paper, and it is worth reading. There is much of value in this paper. Theirs is not a perfect empirical system in which all the model assumptions are met and in which huge population sizes make stochastic effects negligible. Here is a system one step closer to the messy reality of biology. The struggle to align this system with new theory has been worth the effort. Not only does it give us hope that we might usefully be able to discriminate between classes of invasions using real-world data, but it hints at a rule that Tolstoy might have expressed this way: all pulled invasions are alike, each pushed invasion is pushed in its own way.

References

Bîrzu, G., Matin, S., Hallatschek, O., and Korolev, K. S. (2019). Genetic drift in range expansions is very sensitive to density dependence in dispersal and growth. Ecology Letters, 22(11), 1817-1827. doi: https://doi.org/10.1111/ele.13364
Dahirel, M., Bertin, A., Haond, M., Blin, A., Lombaert, E., Calcagno, V., Fellous, S., Mailleret, L., Malausa, T., and Vercken, E. (2020). Shifts from pulled to pushed range expansions caused by reduction of landscape connectivity. bioRxiv, 2020.05.13.092775, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. https://doi.org/10.1101/2020.05.13.092775
Gandhi, S. R., Korolev, K. S., and Gore, J. (2019). Cooperation mitigates diversity loss in a spatially expanding microbial population. Proceedings of the National Academy of Sciences, 116(47), 23582-23587. doi: https://doi.org/10.1073/pnas.1910075116
Gandhi, S. R., Yurtsev, E. A., Korolev, K. S., and Gore, J. (2016). Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population. Proceedings of the National Academy of Sciences, 113(25), 6922-6927. doi: https://doi.org/10.1073/pnas.1521056113
Haond, M., Morel-Journel, T., Lombaert, E., Vercken, E., Mailleret, L. and Roques, L. (2018). When higher carrying capacities lead to faster propagation (2018), bioRxiv, 307322, ver. 4 peer-reviewed and recommended by Peer Community in Ecology. https://doi.org/10.1101/307322
Miller et al. (2020). Eco‐evolutionary dynamics of range expansion. Ecology, 101(10), e03139. doi: https://doi.org/10.1002/ecy.3139
Roques, L., Garnier, J., Hamel, F., and Klein, E. K. (2012). Allee effect promotes diversity in traveling waves of colonization. Proceedings of the National Academy of Sciences, 109(23), 8828-8833. doi: https://doi.org/10.1073/pnas.1201695109

Shifts from pulled to pushed range expansions caused by reduction of landscape connectivityMaxime Dahirel, Aline Bertin, Marjorie Haond, Aurélie Blin, Eric Lombaert, Vincent Calcagno, Simon Fellous, Ludovic Mailleret, Thibaut Malausa, Elodie Vercken<p>Range expansions are key processes shaping the distribution of species; their ecological and evolutionary dynamics have become especially relevant today, as human influence reshapes ecosystems worldwide. Many attempts to explain and predict ran...Evolutionary Applications, Evolutionary Dynamics, Evolutionary Ecology, Experimental Evolution, Phylogeography & BiogeographyBen Phillips2020-08-04 12:51:56 View
11 Dec 2020
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Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data

Phylodynamics of hepatitis C virus reveals transmission dynamics within and between risk groups in Lyon

Recommended by based on reviews by Chris Wymant and Louis DuPlessis

Genomic epidemiology seeks to better understand the transmission dynamics of infectious pathogens using molecular sequence data. Phylodynamic methods have given genomic epidemiology new power to track the transmission dynamics of pathogens by combining phylogenetic analyses with epidemiological modeling. In recent year, applications of phylodynamics to chronic viral infections such as HIV and hepatitis C virus (HVC) have provided some of the best examples of how phylodynamic inference can provide valuable insights into transmission dynamics within and between different subpopulations or risk groups, allowing for more targeted interventions.
However, conducting phylodynamic inference under complex epidemiological models comes with many challenges. In some cases, it is not always straightforward or even possible to perform likelihood-based inference. Structured SIR-type models where infected individuals can belong to different subpopulations provide a classic example. In this case, the model is both nonlinear and has a high-dimensional state space due to tracking different types of hosts. Computing the likelihood of a phylogeny under such a model involves complex numerical integration or data augmentation methods [1]. In these situations, Approximate Bayesian Computation (ABC) provides an attractive alternative, as Bayesian inference can be performed without computing likelihoods as long as one can efficiently simulate data under the model to compare against empirical observations [2].
Previous work has shown how ABC approaches can be applied to fit epidemiological models to phylogenies [3,4]. Danesh et al. [5] further demonstrate the real world merits of ABC by fitting a structured SIR model to HCV data from Lyon, France. Using this model, they infer viral transmission dynamics between “classical” hosts (typically injected drug users) and “new” hosts (typically young MSM) and show that a recent increase in HCV incidence in Lyon is due to considerably higher transmission rates among “new” hosts . This study provides another great example of how phylodynamic analysis can help epidemiologists understand transmission patterns within and between different risk groups and the merits of expanding our toolkit of statistical methods for phylodynamic inference.

References

[1] Rasmussen, D. A., Volz, E. M., and Koelle, K. (2014). Phylodynamic inference for structured epidemiological models. PLoS Comput Biol, 10(4), e1003570. doi: https://doi.org/10.1371/journal.pcbi.1003570
[2] Beaumont, M. A., Zhang, W., and Balding, D. J. (2002). Approximate Bayesian computation in population genetics. Genetics, 162(4), 2025-2035.
[3] Ratmann, O., Donker, G., Meijer, A., Fraser, C., and Koelle, K. (2012). Phylodynamic inference and model assessment with approximate bayesian computation: influenza as a case study. PLoS Comput Biol, 8(12), e1002835. doi: https://doi.org/10.1371/journal.pcbi.1002835
[4] Saulnier, E., Gascuel, O., and Alizon, S. (2017). Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study. PLoS computational biology, 13(3), e1005416. doi: https://doi.org/10.1371/journal.pcbi.1005416
[5] Danesh, G., Virlogeux, V., Ramière, C., Charre, C., Cotte, L. and Alizon, S. (2020) Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data. bioRxiv, 689158, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: https://doi.org/10.1101/689158

Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence dataGonche Danesh, Victor Virlogeux, Christophe Ramière, Caroline Charre, Laurent Cotte, Samuel Alizon<p>Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fa...Evolutionary Epidemiology, Phylogenetics / PhylogenomicsDavid Rasmussen2019-07-11 13:37:23 View