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23 Jun 2021
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Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift

Separating adaptation from drift: A cautionary tale from a self-fertilizing plant

Recommended by based on reviews by Pierre Olivier Cheptou, Jon Agren and Stefan Laurent

In recent years many studies have documented shifts in phenology in response to climate change, be it in arrival times in migrating birds, budset in trees, adult emergence in butterflies, or flowering time in annual plants (Coen et al. 2018; Piao et al. 2019). While these changes are, in part, explained by phenotypic plasticity, more and more studies find that they involve also genetic changes, that is, they involve evolutionary change (e.g., Metz et al. 2020). Yet, evolutionary change may occur through genetic drift as well as selection. Therefore, in order to demonstrate adaptive evolutionary change in response to climate change, drift has to be excluded as an alternative explanation (Hansen et al. 2012). A new study by Gay et al. (2021) shows just how difficult this can be. 

The authors investigated a recent evolutionary shift in flowering time by in a population an annual plant that reproduces predominantly by self-fertilization. The population has recently been subjected to increased temperatures and reduced rainfalls both of which are believed to select for earlier flowering times. They used a “resurrection” approach (Orsini et al. 2013; Weider et al. 2018): Genotypes from the past (resurrected from seeds) were compared alongside more recent genotypes (from more recently collected seeds) under identical conditions in the greenhouse. Using an experimental design that replicated genotypes, eliminated maternal effects, and controlled for microenvironmental variation, they found said genetic change in flowering times: Genotypes obtained from recently collected seeds flowered significantly (about 2 days) earlier than those obtained 22 generations before. However, neutral markers (microsatellites) also showed strong changes in allele frequencies across the 22 generations, suggesting that effective population size, Ne, was low (i.e., genetic drift was strong), which is typical for highly self-fertilizing populations. In addition, several multilocus genotypes were present at high frequencies and persisted over the 22 generations, almost as in clonal populations (e.g., Schaffner et al. 2019). The challenge was thus to evaluate whether the observed evolutionary change was the result of an adaptive response to selection or may be explained by drift alone. 

Here, Gay et al. (2021) took a particularly careful and thorough approach. First, they carried out a selection gradient analysis, finding that earlier-flowering plants produced more seeds than later-flowering plants. This suggests that, under greenhouse conditions, there was indeed selection for earlier flowering times. Second, investigating other populations from the same region (all populations are located on the Mediterranean island of Corsica, France), they found that a concurrent shift to earlier flowering times occurred also in these populations. Under the hypothesis that the populations can be regarded as independent replicates of the evolutionary process, the observation of concurrent shifts rules out genetic drift (under drift, the direction of change is expected to be random). 

The study may well have stopped here, concluding that there is good evidence for an adaptive response to selection for earlier flowering times in these self-fertilizing plants, at least under the hypothesis that selection gradients estimated in the greenhouse are relevant to field conditions. However, the authors went one step further. They used the change in the frequencies of the multilocus genotypes across the 22 generations as an estimate of realized fitness in the field and compared them to the phenotypic assays from the greenhouse. The results showed a tendency for high-fitness genotypes (positive frequency changes) to flower earlier and to produce more seeds than low-fitness genotypes. However, a simulation model showed that the observed correlations could be explained by drift alone, as long as Ne is lower than ca. 150 individuals. The findings were thus consistent with an adaptive evolutionary change in response to selection, but drift could only be excluded as the sole explanation if the effective population size was large enough. 

The study did provide two estimates of Ne (19 and 136 individuals, based on individual microsatellite loci or multilocus genotypes, respectively), but both are problematic. First, frequency changes over time may be influenced by the presence of a seed bank or by immigration from a genetically dissimilar population, which may lead to an underestimation of Ne (Wang and Whitlock 2003). Indeed, the low effective size inferred from the allele frequency changes at microsatellite loci appears to be inconsistent with levels of genetic diversity found in the population. Moreover, high self-fertilization reduces effective recombination and therefore leads to non-independence among loci. This lowers the precision of the Ne estimates (due to a higher sampling variance) and may also violate the assumption of neutrality due to the possibility of selection (e.g., due to inbreeding depression) at linked loci, which may be anywhere in the genome in case of high degrees of self-fertilization. 

There is thus no definite answer to the question of whether or not the observed changes in flowering time in this population were driven by selection. The study sets high standards for other, similar ones, in terms of thoroughness of the analyses and care in interpreting the findings. It also serves as a very instructive reminder to carefully check the assumptions when estimating neutral expectations, especially when working on species with complicated demographies or non-standard life cycles. Indeed the issues encountered here, in particular the difficulty of establishing neutral expectations in species with low effective recombination, may apply to many other species, including partially or fully asexual ones (Hartfield 2016). Furthermore, they may not be limited to estimating Ne but may also apply, for instance, to the establishment of neutral baselines for outlier analyses in genome scans (see e.g, Orsini et al. 2012). 

References

Cohen JM, Lajeunesse MJ, Rohr JR (2018) A global synthesis of animal phenological responses to climate change. Nature Climate Change, 8, 224–228. https://doi.org/10.1038/s41558-018-0067-3

Gay L, Dhinaut J, Jullien M, Vitalis R, Navascués M, Ranwez V, Ronfort J (2021) Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift. bioRxiv, 2020.08.21.261230, ver. 4 recommended and peer-reviewed by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2020.08.21.261230

Hansen MM, Olivieri I, Waller DM, Nielsen EE (2012) Monitoring adaptive genetic responses to environmental change. Molecular Ecology, 21, 1311–1329. https://doi.org/10.1111/j.1365-294X.2011.05463.x

Hartfield M (2016) Evolutionary genetic consequences of facultative sex and outcrossing. Journal of Evolutionary Biology, 29, 5–22. https://doi.org/10.1111/jeb.12770

Metz J, Lampei C, Bäumler L, Bocherens H, Dittberner H, Henneberg L, Meaux J de, Tielbörger K (2020) Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment. Ecology Letters, 23, 1643–1653. https://doi.org/10.1111/ele.13596

Orsini L, Schwenk K, De Meester L, Colbourne JK, Pfrender ME, Weider LJ (2013) The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments. Trends in Ecology & Evolution, 28, 274–282. https://doi.org/10.1016/j.tree.2013.01.009

Orsini L, Spanier KI, Meester LD (2012) Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolution. Molecular Ecology, 21, 2160–2175. https://doi.org/10.1111/j.1365-294X.2011.05429.x

Piao S, Liu Q, Chen A, Janssens IA, Fu Y, Dai J, Liu L, Lian X, Shen M, Zhu X (2019) Plant phenology and global climate change: Current progresses and challenges. Global Change Biology, 25, 1922–1940. https://doi.org/10.1111/gcb.14619

Schaffner LR, Govaert L, De Meester L, Ellner SP, Fairchild E, Miner BE, Rudstam LG, Spaak P, Hairston NG (2019) Consumer-resource dynamics is an eco-evolutionary process in a natural plankton community. Nature Ecology & Evolution, 3, 1351–1358. https://doi.org/10.1038/s41559-019-0960-9

Wang J, Whitlock MC (2003) Estimating Effective Population Size and Migration Rates From Genetic Samples Over Space and Time. Genetics, 163, 429–446. PMID: 12586728

Weider LJ, Jeyasingh PD, Frisch D (2018) Evolutionary aspects of resurrection ecology: Progress, scope, and applications—An overview. Evolutionary Applications, 11, 3–10. https://doi.org/10.1111/eva.12563

Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic driftLaurène Gay, Julien Dhinaut, Margaux Jullien, Renaud Vitalis, Miguel Navascués, Vincent Ranwez, and Joëlle Ronfort<p style="text-align: justify;">Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these traits modifications correlate with the environmental changes that occurred during the time ...Adaptation, Evolutionary Ecology, Genotype-Phenotype, Phenotypic Plasticity, Population Genetics / Genomics, Quantitative Genetics, Reproduction and SexChristoph Haag2020-08-21 17:26:59 View
11 Jul 2022
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Mutualists construct the ecological conditions that trigger the transition from parasitism

Give them some space: how spatial structure affects the evolutionary transition towards mutualistic symbiosis

Recommended by ORCID_LOGO based on reviews by Eva Kisdi and 3 anonymous reviewers

The evolution of mutualistic symbiosis is a puzzle that has fascinated evolutionary ecologist for quite a while. Data on transitions between symbiotic bacterial ways of life has evidenced shifts from mutualism towards parasitism and vice versa (Sachs et al., 2011), so there does not seem to be a strong determinism on those transitions. From the host’s perspective, mutualistic symbiosis implies at the very least some form of immune tolerance, which can be costly (e.g. Sorci, 2013). Empirical approaches thus raise very important questions: How can symbiosis turn from parasitism into mutualism when it seemingly needs such a strong alignment of selective pressures on both the host and the symbiont? And yet why is mutualistic symbiosis so widespread and so important to the evolution of macro-organisms (Margulis, 1998)?

While much of the theoretical literature on the evolution of symbiosis and mutualism has focused on either the stability of such relationships when non-mutualists can invade the host-symbiont system (e.g. Ferrière et al., 2007) or the effect of the mode of symbiont transmission on the evolutionary dynamics of mutualism (e.g. Genkai-Kato and Yamamura, 1999), the question remains whether and under which conditions parasitic symbiosis can turn into mutualism in the first place. Earlier results suggested that spatial demographic heterogeneity between host populations could be the leading determinant of evolution towards mutualism or parasitism (Hochberg et al., 2000). Here, Ledru et al. (2022) investigate this question in an innovative way by simulating host-symbiont evolutionary dynamics in a spatially explicit context. Their hypothesis is intuitive but its plausibility is difficult to gauge without a model: Does the evolution towards mutualism depend on the ability of the host and symbiont to evolve towards close-range dispersal in order to maintain clusters of efficient host-symbiont associations, thus outcompeting non-mutualists?

I strongly recommend reading this paper as the results obtained by the authors are very clear: competition strength and the cost of dispersal both affect the likelihood of the transition from parasitism to mutualism, and once mutualism has set in, symbiont trait values clearly segregate between highly dispersive parasites and philopatric mutualists. The demonstration of the plausibility of their hypothesis is accomplished with brio and thoroughness as the authors also examine the conditions under which the transition can be reversed, the impact of the spatial range of competition and the effect of mortality. Since high dispersal cost and strong, long-range competition appear to be the main factors driving the evolutionary transition towards mutualistic symbiosis, now is the time for empiricists to start investigating this question with spatial structure in mind.

References

Ferrière, R., Gauduchon, M. and Bronstein, J. L. (2007) Evolution and persistence of obligate mutualists and exploiters: competition for partners and evolutionary immunization. Ecology Letters, 10, 115-126. https://doi.org/10.1111/j.1461-0248.2006.01008.x

Genkai-Kato, M. and Yamamura, N. (1999) Evolution of mutualistic symbiosis without vertical transmission. Theoretical Population Biology, 55, 309-323. https://doi.org/10.1006/tpbi.1998.1407

Hochberg, M. E., Gomulkiewicz, R., Holt, R. D. and Thompson, J. N. (2000) Weak sinks could cradle mutualistic symbioses - strong sources should harbour parasitic symbioses. Journal of Evolutionary Biology, 13, 213-222. https://doi.org/10.1046/j.1420-9101.2000.00157.x

Ledru L, Garnier J, Rohr M, Noûs C and Ibanez S (2022) Mutualists construct the ecological conditions that trigger the transition from parasitism. bioRxiv, 2021.08.18.456759, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.08.18.456759

Margulis, L. (1998) Symbiotic planet: a new look at evolution, Basic Books, Amherst.

Sachs, J. L., Skophammer, R. G. and Regus, J. U. (2011) Evolutionary transitions in bacterial symbiosis. Proceedings of the National Academy of Sciences, 108, 10800-10807. https://doi.org/10.1073/pnas.1100304108

Sorci, G. (2013) Immunity, resistance and tolerance in bird–parasite interactions. Parasite Immunology, 35, 350-361. https://doi.org/10.1111/pim.12047

Mutualists construct the ecological conditions that trigger the transition from parasitismLeo Ledru, Jimmy Garnier, Matthias Rohr, Camille Nous, Sebastien Ibanez<p>The evolution of mutualism between hosts and initially parasitic symbionts represents a major transition in evolution. Although vertical transmission of symbionts during host reproduction and partner control both favour the stability of mutuali...Evolutionary Ecology, Species interactionsFrancois Massol2021-08-20 12:25:40 View
03 Oct 2023
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The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer model

Evolution and consequences of plastic foraging behavior in consumer-resource ecosystems

Recommended by based on reviews by 2 anonymous reviewers

Plastic responses of organisms to their environment may be maladaptive in particular when organisms are exposed to new environments. Phenotypic plasticity may also have opposite effects on the adaptive response of organisms to environmental changes: whether phenotypic plasticity favors or hinders such adaptation depends on a balance between the ability of the population to respond to the change non-genetically in the short term, and the weakened genetic response to environmental change. These topics have received continued attention, particularly in the context of climate change (e.g., Chevin et al. 2013, Duputié et al., 2015, Vinton et al . 2022).

In their work, Ledru et al. focus on the adaptive nature of plastic behavior and on its consequences in a consumer-resource ecosystem. As they emphasize, previous works have found that plastic foraging promotes community stability, but these did not consider plasticity as an evolving trait, so Ledru et al. set out to test whether this conclusion holds when both plastic foraging and niche traits of consumers and resources evolve (though ultimately, their new conclusions may not all depend on plasticity evolving). Along the way, they first seek to clarify when such plasticity will evolve, and how it affects the evolution of the niche diversity of consumers and resources, before turning to the question of consumer persistence. 

The model is rather complex, as three traits are allowed to evolve, and the resource uptake expressed through plastic behavior has its own dynamics affected by some form of social learning. Classically, in models of niche evolution, a consumer's efficiency in exploiting a resource characterized by a trait y (here, the resource's individual niche trait), has been described in terms of location-scale (typically Gaussian) kernels, with mean x (the consumer's individual niche trait) specifying the most efficiently exploited resource, and with variance characterizing individual niche breadth. The evolution of the variance has been considered in some previous models but is assumed to be fixed here.  Rather, the new model considers the evolution of the distribution of resource traits, of the consumer's individual niche trait (which is not plastic), and of a "plastic foraging trait" that controls the relative time spent foraging plastically versus foraging randomly. When foraging plastically, the consumers modify their foraging effort towards the type of resource that maximizes their energy intake. in some previous models, the effect of variation in the extent of plastic foraging was already considered, but the evolution of allocation to a plastic foraging strategy versus random foraging was not considered. The model is formulated through reaction-diffusion equations, and its dynamics is investigated by numerical integration.

Foraging plasticity readily evolves, when resources vary widely enough, competition for resources is strong, and the cost of plasticity is weak. This means in particular that a large individual niche width of consumers selects for increased plastic foraging, as the evolution of plastic foraging leads to reduced niche overlap between consumers. The evolution of plastic foraging itself generally, though not always, favors the diversification of the niche traits of consumers and of resources. There is thus a positive feedback loop between plastic foraging and resource diversity. Ledru et al. conclude that the total niche width of the consumer population should also correlate with the evolution of plastic foraging, an implication which they relate to the so-called niche variation hypothesis and to empirical tests of it. 

The joint evolution of the consumer's individual niche trait and plastic foraging trait generates a striking pattern within populations: consumers whose individual niche trait is at an edge of the resource distribution forage more plastically. The authors observe that this relatively simple prediction has not been subjected to any empirical test. 

Returning to the question of consumer persistence, Ledru et al. evaluate this persistence when consumer mortality increases, and in response to either gradual or sudden environmental changes. These different perturbations all reduce the benefits of plastic foraging. The effect of plastic foraging on stability are complex, being negative or positive effect depending on the type of disturbance, and in particular the ecosystem has a lower sustainable rate of environmental change in the presence of plastic foraging. However, allowing the evolutionary regression of plastic foraging then has a comparatively positive effect on persistence.

Despite the substantial effort devoted to analyzing this complex model, relaxing some of its assumptions would likely reveal further complexities. Notably, the overall effect of plasticity on consumer persistence depends on effects already encountered in models of the adaptive response of single species to environmental change: a fast non-genetic response in the short term versus a weakened genetic response in the longer term. The overall balance between these opposite effects on adaptation may be difficult to predict robustly. In the case of a constant rate of environmental change, the results of the present model depend on a lag load between the trait changes of consumer and resource populations, and the extent of the lag may also depend on many factors, such as the extent of genetic variation (e.g., Bürger & Lynch, 1995) for niche traits in consumers and resources. Here, the same variance of mutational effects was assumed for all three evolving traits. Further, spatial environmental variation, a central issue in studies of adaptive responses to environmental changes (e.g., Parmesan, 2006, Zhu et al., 2012), was not considered. Finally, the rate of adjustment of effort by consumers with given niche trait and plastic foraging trait values was assumed proportional to the density of consumers with such trait values. This was justified as a way of accounting for the use of social cues during foraging, but to the extent that they occur, social effects could manifest themselves through other learning dynamics. 

In conclusion, Ledru et al. have addressed a broad range of questions, suggesting new empirical tests of behavioural patterns on one side, and recovering in the context of community response to environmental changes a complexity that could be expected from earlier works on adaptive responses of organisms but that has been overlooked by previous works on community effects of phenotypic plasticity.

References

Bürger, R. and Lynch, M. (1995), Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution, 49: 151-163. https://doi.org/10.1111/j.1558-5646.1995.tb05967.x

Chevin, L.-M., Collins, S. and Lefèvre, F. (2013), Phenotypic plasticity and evolutionary demographic responses to climate change: taking theory out to the field. Funct Ecol, 27: 967-979. https://doi.org/10.1111/j.1365-2435.2012.02043.x

Duputié, A., Rutschmann, A., Ronce, O. and Chuine, I. (2015), Phenological plasticity will not help all species adapt to climate change. Glob Change Biol, 21: 3062-3073. https://doi-org.inee.bib.cnrs.fr/10.1111/gcb.12914

Ledru, L., Garnier, J., Guillot, O., Faou, E., & Ibanez, S. (2023). The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer model. EcoEvoRxiv, ver. 4 peer-reviewed and recommended by Peer Community In Evolutionary Biology. https://doi.org/10.32942/X2QG7M

Parmesan, C. (2006) Ecological and evolutionary responses to recent climate change
Annual Review of Ecology, Evolution, and Systematics 2006 37:1, 637-669. https://doi.org/10.1146/annurev.ecolsys.37.091305.110100

Vinton, A.C., Gascoigne, S.J.L., Sepil, I., Salguero-Gómez, R., (2022) Plasticity’s role in adaptive evolution depends on environmental change components. Trends in Ecology & Evolution, 37: 1067-1078.
https://doi.org/10.1016/j.tree.2022.08.008

Zhu, K., Woodall, C.W. and Clark, J.S. (2012), Failure to migrate: lack of tree range expansion in response to climate change. Glob Change Biol, 18: 1042-1052. https://doi.org/10.1111/j.1365-2486.2011.02571.x

The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer modelLéo Ledru, Jimmy Garnier, Océane Guillot, Erwan Faou, Camille Noûs, Sébastien Ibanez<p style="text-align: justify;">Phenotypic plasticity has important ecological and evolutionary consequences. In particular, behavioural phenotypic plasticity such as plastic foraging (PF) by consumers, may enhance community stability. Yet little ...Bioinformatics & Computational Biology, Evolutionary Dynamics, Evolutionary Ecology, Phenotypic PlasticityFrançois Rousset2023-03-25 12:04:08 View
19 Mar 2018
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Natural selection on plasticity of thermal traits in a highly seasonal environment

Is thermal plasticity itself shaped by natural selection? An assessment with desert frogs

Recommended by based on reviews by Dries Bonte, Wolf Blanckenhorn and Nadia Aubin-Horth

It is well known that climatic factors – most notably temperature, season length, insolation and humidity – shape the thermal niche of organisms on earth through the action of natural selection. But how is this achieved precisely? Much of thermal tolerance is actually mediated by phenotypic plasticity (as opposed to genetic adaptation). A prominent expectation is that environments with greater (daily and/or annual) thermal variability select for greater plasticity, i.e. better acclimation capacity. Thus, plasticity might be selected per se.

A Chilean group around Leonardo Bacigalupe assessed natural selection in the wild in one marginal (and extreme) population of the four-eyed frog Pleurodema thaul (Anura: Leptodactylidae) in an isolated oasis in the Atacama Desert, permitting estimation of mortality without much potential of confounding it with migration [1]. Several thermal traits were considered: CTmax – the critical maximal temperature; CTmin – the critical minimum temperature; Tpref – preferred temperature; Q10 – thermal sensitivity of metabolism; and body mass. Animals were captured in the wild and subsequently assessed for thermal traits in the laboratory at two acclimation temperatures (10° & 20°C), defining the plasticity in all traits as the difference between the traits at the two acclimation temperatures. Thereafter the animals were released again in their natural habitat and their survival was monitored over the subsequent 1.5 years, covering two breeding seasons, to estimate viability selection in the wild. The authors found and conclude that, aside from larger body size increasing survival (an unsurprising result), plasticity does not seem to be systematically selected directly, while some of the individual traits show weak signs of selection.

Despite limited sample size (ca. 80 frogs) investigated in only one marginal but very seasonal population, this study is interesting because selection on plasticity in physiological thermal traits, as opposed to selection on the thermal traits themselves, is rarely investigated. The study thus also addressed the old but important question of whether plasticity (i.e. CTmax-CTmin) is a trait by itself or an epiphenomenon defined by the actual traits (CTmax and CTmin) [2-5]. Given negative results, the main question could not be ultimately solved here, so more similar studies should be performed.

References

[1] Bacigalupe LD, Gaitan-Espitia, JD, Barria AM, Gonzalez-Mendez A, Ruiz-Aravena M, Trinder M & Sinervo B. 2018. Natural selection on plasticity of thermal traits in a highly seasonal environment. bioRxiv 191825, ver. 5 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/191825
[2] Scheiner SM. 1993. Genetics and evolution of phenotypic plasticity. Annual Review in Ecology and Systematics 24: 35–68. doi: 10.1146/annurev.es.24.110193.000343
[3] Scheiner SM. 1993. Plasticity as a selectable trait: Reply to Via. The American Naturalist. 142: 371–373. doi: 10.1086/285544
[4] Via S. 1993. Adaptive phenotypic plasticity - Target or by-product of selection in a variable environment? The American Naturalist. 142: 352–365. doi: 10.1086/285542
[5] Via S. 1993. Regulatory genes and reaction norms. The American Naturalist. 142: 374–378. doi: 10.1086/285542

Natural selection on plasticity of thermal traits in a highly seasonal environmentLeonardo Bacigalupe, Juan Diego Gaitan-Espitia, Aura M Barria, Avia Gonzalez-Mendez, Manuel Ruiz-Aravena, Mark Trinder, Barry Sinervo<p>For ectothermic species with broad geographical distributions, latitudinal/altitudinal variation in environmental temperatures (averages and extremes) are expected to shape the evolution of physiological tolerances and the acclimation capacity ...Adaptation, Evolutionary Ecology, Phenotypic PlasticityWolf Blanckenhorn2017-09-22 23:17:40 View
12 Apr 2017
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Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes

Vectors as motors (of virus evolution)

Recommended by and

Many viruses are transmitted by biological vectors, i.e. organisms that transfer the virus from one host to another. Dengue virus (DENV) is one of them. Dengue is a mosquito-borne viral disease that has rapidly spread around the world since the 1940s. One recent estimate indicates 390 million dengue infections per year [1]. As many arthropod-borne vertebrate viruses, DENV has to cross several anatomical barriers in the vector, to multiply in its body and to invade its salivary glands before getting transmissible. As a consequence, vectors are not passive carriers but genuine hosts of the viruses that potentially have important effects on the composition of virus populations and, ultimately, on virus epidemiology and virulence. Within infected vectors, virus populations are expected to acquire new mutations and to undergo genetic drift and selection effects. However, the intensity of these evolutionary forces and the way they shape virus genetic diversity are poorly known.

In their study, Lequime et al. [2] finely disentangled the effects of genetic drift and selection on DENV populations during their infectious cycle within mosquito (Aedes aegypti) vectors. They evidenced that the genetic diversity of viruses within their vectors is shaped by genetic drift, selection and vector genotype. The experimental design consisted in artificial acquisition of purified virus by mosquitoes during a blood meal. The authors monitored the diversity of DENV populations in Ae. aegypti individuals at different time points by high-throughput sequencing (HTS). They estimated the intensity of genetic drift and selection effects exerted on virus populations by comparing the DENV diversity at these sampling time points with the diversity in the purified virus stock (inoculum).

Disentangling the effects of genetic drift and selection remains a methodological challenge because both evolutionary forces operate concomitantly and both reduce genetic diversity. However, selection reduces diversity in a reproducible manner among experimental replicates (here, mosquito individuals): the fittest variants are favoured at the expense of the weakest ones. In contrast, genetic drift reduces diversity in a stochastic manner among replicates. Genetic drift acts equally on all variants irrespectively of their fitness. The strength of genetic drift is frequently evaluated with the effective population size Ne: the lower Ne, the stronger the genetic drift [3]. The estimation of the effective population size of DENV populations by Lequime et al. [2] was based on single-nucleotide polymorphisms (SNPs) that were (i) present both in the inoculum and in the virus populations sampled at the different time points and (ii) that were neutral (or nearly-neutral) and therefore subjected to genetic drift only and insensitive to selection. As expected for viruses that possess small and constrained genomes, such neutral SNPs are extremely rare. Starting from a set of >1800 SNPs across the DENV genome, only three SNPs complied with the neutrality criteria and were enough represented in the sequence dataset for a precise Ne estimation. Using the method described by Monsion et al. [4], Lequime et al. [2] estimated Ne values ranging from 5 to 42 viral genomes (95% confidence intervals ranged from 2 to 161 founding viral genomes). Consequently, narrow bottlenecks occurred at the virus acquisition step, since the blood meal had allowed the ingestion of ca. 3000 infectious virus particles, on average. Interestingly, bottleneck sizes did not differ between mosquito genotypes. Monsion et al.’s [4] formula provides only an approximation of Ne. A corrected formula has been recently published [5]. We applied this exact Ne formula to the means and variances of the frequencies of the three neutral markers estimated before and after the bottlenecks (Table 1 in [2]), and nearly identical Ne estimates were obtained with both formulas.

Selection intensity was estimated from the dN/dS ratio between the nonsynonymous and synonymous substitution rates using the HTS data on DENV populations. DENV genetic diversity increased following initial infection but was restricted by strong purifying selection during virus expansion in the midgut. Again, no differences were detected between mosquito genotypes. However and importantly, significant differences in DENV genetic diversity were detected among mosquito genotypes. As they could not be related to differences in initial genetic drift or to selection intensity, the authors raise interesting alternative hypotheses, including varying rates of de novo mutations due to differences in replicase fidelity or differences in the balancing selection regime. Interestingly, they also suggest that this observation could simply result from a methodological issue linked to the detection threshold of low-frequency SNPs.
 

References

[1] Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, et al. 2013. The global distribution and burden of dengue. Nature 496: 504–7 doi: 10.1038/nature12060

[2] Lequime S, Fontaine A, Gouilh MA, Moltini-Conclois I and Lambrechts L. 2016. Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes. PloS Genetics 12: e1006111 doi: 10.1371/journal.pgen.1006111

[3] Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics 10: 195-205 doi: 10.1038/nrg2526

[4] Monsion B, Froissart R, Michalakis Y and Blanc S. 2008. Large bottleneck size in cauliflower mosaic virus populations during host plant colonization. PloS Pathogens 4: e1000174 doi: 10.1371/journal.ppat.1000174

[5] Thébaud G and Michalakis Y. 2016. Comment on ‘Large bottleneck size in cauliflower mosaic virus populations during host plant colonization’ by Monsion et al. (2008). PloS Pathogens 12: e1005512 doi: 10.1371/journal.ppat.1005512

Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoesLequime S, Fontaine A, Gouilh MA, Moltini-Conclois I and Lambrechts LDue to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically re...Evolutionary Dynamics, Molecular Evolution, Population Genetics / GenomicsFrédéric Fabre2017-04-10 14:26:04 View
29 Nov 2023
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Does sociality affect evolutionary speed?

On the evolutionary implications of being a social animal

Recommended by based on reviews by Rafael Lucas Rodriguez and 1 anonymous reviewer

What does it mean to be highly social?  Considering the so-called four ‘pinnacles’ of animal society (Wilson, 1975) – humans, cooperative breeding as found in some non-human mammals and birds, the social insects, and colonial marine invertebrates – having inter-individual relations extending beyond the sexual pair and the parent-offspring interaction is foremost.  In many cases being social implies a high local population density, interaction with the same group of individuals over an extended time period, and an overlapping of generations.  Additional features of social species may be a wide geographical range, perhaps associated with ecological and behavioral plasticity, the latter often facilitated by cultural transmission of traditions.  

Narrowing our perspective to the domain of PCI Evolutionary Biology, we might continue our question by asking whether being social predisposes one to a special evolutionary path toward the future.  Do social species evolve faster (or slower) than their more solitary relatives such that over time they are more unlike (or similar to) those relatives (anagenesis)?  And are evolutionary changes in social species more or less likely to be accompanied by lineage splitting (cladogenesis) and ultimately speciation?  The latter question is parallel to one first posed over 40 years ago (West-Eberhard, 1979; Lande, 1981) for sexually selected traits:  Do strong mating preferences and conspicuous courtship signals generate speciation via the Fisherian process or ecological divergence?  An extensive survey of birds had found little supporting evidence (Price, 1998), but a recent one that focused on plumage complexity in tanagers did reveal a relationship, albeit a weak one (Price-Waldman et al., 2020).  Because sexual selection has been viewed as a part of the broader process of social selection (West-Eberhard, 1979), it is thus fitting to extend our surveys to the evolutionary implications of being social.

Unlike the inquiry for a sexual selection - evolutionary change connection, a social behavior counterpart has remained relatively untreated.  Diverse logistical problems might account for this oversight.  What objective proxies can be used for social behavior, and for the rate of evolutionary change within a lineage?  How many empirical studies have generated data from which appropriate proxies could be extracted?  More intractable is the conundrum arising from the connectedness between socially- and sexually-selected traits.  For example, the elevated population density found in highly social species can greatly increase the mating advantage enjoyed by an attractive male.  If anagenesis is detected, did it result from social behavior or sexual selection?  And if social behavior leads to a group structure in which male-male competition is reduced, would a modest rate of evolutionary change be support for the sexual selection - evolutionary speed connection or evidence opposing the sociality - evolution one?

Against the above odds, several biologists have begun to explore the notion that social behavior just might favor evolutionary speed in either anagenesis or cladogenesis.  In a recent analysis relying on the comparative method, Lluís Socias-Martínez and Louise Rachel Peckre (2023) combed the scientific literature archives and identified those studies with specific data on the relationships between sexual selection or social behavior and evolutionary change, either anagenesis or cladogenesis.  The authors were careful to employ fairly conservative criteria for including studies, and the number eventually retained was small.  Nonetheless, some patterns emerge:  Many more studies report anagenesis than cladogenesis, and many more report correlations with sexually-selected traits than with non-sexual social behavior ones.  And, no study indicates a potential effect of social behavior on cladogenesis.  Is this latter observation authentic or an artifact of a paucity of data?  There are some a priori reasons why cladogenesis may seldom arise.  Whereas highly social behavior could lead to fission encompassing mutually isolated population clusters within a species, social behavior may also engender counterbalancing plasticity that allows and even promotes inter-cluster migration and fusion.  And briefly – and non-systematically, as the rate of lineage splitting would need to be measured – looking at one of the pinnacles of animal social behavior, the social insects, there is little indication that diversification has been accelerated.  There are fewer than 3000 described species of termites, only ca. 16,000 ants, and the vast majority of bees and wasps are solitary.                            

Lluís Socias-Martínez and Louise Rachel Peckre provide us with a very detailed discussion of these and a myriad of other complications.  I end with a common refrain, we need more consideration of the authors’ interesting question, and much more data and analysis.  One can thank Socias-Martínez and Peckre for pointing us in that direction.

References

Lande, R. (1981). Models of speciation by sexual selection on polygenic traits. Proc. Natn. Acad. Sci. USA 78, 3721-3725. https://doi.org/10.1073/pnas.78.6.3721

Price, T. (1998). Sexual selection and natural selection in bird speciation. Phil. Trans. Roy. Soc. B, 353, 251-260.  https://doi.org/10.1098/rstb.1998.0207  

Price‐Waldman, R. M., Shultz, A. J., & Burns, K. J. (2020). Speciation rates are correlated with changes in plumage color complexity in the largest family of songbirds. Evolution, 74(6), 1155–1169. https://doi.org/10.1111/evo.13982

Socias-Martínez and Peckre. (2023). Does sociality affect evolutionary speed? Zenodo, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.5281/zenodo.10086186

West-Eberhard, M. J. (1979). Sexual selection, social competition, and evolution. Proceedings of the American Philosophical Society, 123(4), 222–234. http://www.jstor.org/stable/2828804

Wilson, E. O. (1975). Sociobiology. The New Synthesis. Cambridge, Mass., The Belknap Press of Harvard University

Does sociality affect evolutionary speed?Lluís Socias-Martínez, Louise Rachel Peckre<p>An overlooked source of variation in evolvability resides in the social lives of animals. In trying to foster research in this direction, we offer a critical review of previous work on the link between evolutionary speed and sociality. A first ...Behavior & Social Evolution, Evolutionary Dynamics, Evolutionary Theory, Genome Evolution, Macroevolution, Molecular Evolution, Population Genetics / Genomics, Sexual Selection, SpeciationMichael D Greenfield2023-03-03 00:10:49 View
16 Mar 2023
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Phylogeographic breaks and how to find them: Separating vicariance from isolation by distance in a lizard with restricted dispersal

The difficult task of partitioning the effects of vicariance and isolation by distance in poor dispersers

Recommended by ORCID_LOGO based on reviews by Kevin Sánchez and Aglaia (Cilia) Antoniou

Partitioning the effects of vicariance and low dispersal has been a long-standing problem in historical biogeography and phylogeography. While the term “vicariance” refers to divergence in allopatry, caused by some physical (geological, geographical) or climatic barriers (e.g. Rosen 1978), isolation by distance refers to the genetic differentiation of remote populations due to the physical distance separating them, when the latter surpasses the scale of dispersal (Wright 1938, 1940, 1943). 

Vicariance and dispersal have long been considered as separate forces leading to separate scenarii of speciation (e.g. reviewed in Hickerson and Meyer 2008). Nevertheless, these two processes are strongly linked, as, for example, vicariance theory relies on the assumption that ancestral lineages were once linked by dispersal prior to physical or climatic isolation (Rosen 1978). Low dispersal and vicariance are not mutually exclusive, and distinguishing these two processes in heterogeneous landscapes, especially for poor dispersers, remains therefore a severe challenge. For example, low dispersal (and/or small population size) can give rise to geographic patterns consistent with a phylogeographic break and be mistaken for geographic isolation (Irwin 2002, Kuo and Avise 2005).

The study of Rancilliac and colleagues (2023) is at the heart of this issue. It focuses on a nominal lizard species, the red-tailed spiny-footed lizard (Acanthodactylus erythrurus, Squamata: Lacertidae), which has a wide spatial distribution (from the Maghreb to the Iberian Peninsula), is found in a variety of different habitats, and has a wide range of morphological traits that do not always correlate with phylogeny. The main question is the following: have “the morphological and ecological diversification of this group been produced by vicariance and lineage diversification, or by local adaptation in the face of historical gene flow?” To tackle this question, the authors used sequence data from multiple mitochondrial and nuclear markers and a nested analysis workflow integrating phylogeography, multiple correspondence analyses and a relatively novel approach to IBD testing (Hausdorf & Henning, 2020). The latter is based on regression analysis and was shown to be less prone to error than the traditional (partial) Mantel test. 

While this set of methods allowed the partitioning of the effect of isolation by distance and vicariance in shaping contemporary genetic diversity in red-tailed spiny-footed lizards, some of the evolutionary history of this species complex remains blurred by ongoing gene flow and admixture, retention of ancestral polymorphism, or selection. The lack of congruence between mitochondrial and nuclear gene trees once again warns us that proposing evolutionary scenarii based on individual gene trees is a risky business. 

References

Hausdorf B, Hennig C (2020) Species delimitation and geography. Molecular Ecology Resources, 20, 950–960. https://doi.org/10.1111/1755-0998.13184

Hickerson MJ, Meyer CP (2008) Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. BMC Evolutionary Biology, 8, 322. https://doi.org/10.1186/1471-2148-8-322

Irwin DE (2002) Phylogeographic breaks without geographic barriers to gene flow. Evolution, 56, 2383–2394. https://doi.org/10.1111/j.0014-3820.2002.tb00164.x

Kuo C-H, Avise JC (2005) Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica, 124, 179–186. https://doi.org/10.1007/s10709-005-2095-y

Rancilhac L, Miralles A, Geniez P, Mendez-Aranda D, Beddek M, Brito JC, Leblois R, Crochet P-A (2023) Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal. bioRxiv, 2022.09.30.510256, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.09.30.510256

Rosen DE (1978) Vicariant Patterns and Historical Explanation in Biogeography. Systematic Biology, 27, 159–188. https://doi.org/10.2307/2412970

Wright, S (1938) Size of population and breeding structure in relation to evolution. Science 87:430-431.

Wright S (1940) Breeding Structure of Populations in Relation to Speciation. The American Naturalist, 74, 232–248. https://doi.org/10.1086/280891

Wright S (1943) Isolation by distance. Genetics, 28, 114–138. https://doi.org/10.1093/genetics/28.2.114

Phylogeographic breaks and how to find them: Separating vicariance from isolation by distance in a lizard with restricted dispersalLoïs Rancilhac, Aurélien Miralles, Philippe Geniez, Daniel Mendez-Arranda, Menad Beddek, José Carlos Brito, Raphaël Leblois, Pierre-André Crochet<p>Aim</p> <p>Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise...Phylogeography & Biogeography, Population Genetics / Genomics, Speciation, Systematics / TaxonomyEric Pante Kevin Sánchez2022-10-05 13:11:28 View
18 Nov 2020
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A demogenetic agent based model for the evolution of traits and genome architecture under sexual selection

Sexual selection goes dynamic

Recommended by based on reviews by Frédéric Guillaume and 1 anonymous reviewer

150 years after Darwin published ‘Descent of man and selection in relation to sex’ (Darwin, 1871), the evolutionary mechanism that he laid out in his treatise continues to fascinate us. Sexual selection is responsible for some of the most spectacular traits among animals, and plants, and it appeals to our interest in all things reproductive and sexual (Bell, 1982). In addition, sexual selection poses some of the more intractable problems in evolutionary biology: Its realm encompasses traits that are subject to markedly different selection pressures, particularly when distinct, yet associated, traits tend to be associated with males, e.g. courtship signals, and with females, e.g. preferences (cf. Ah-King & Ahnesjo, 2013). While separate, such traits cannot evolve independently of each other (Arnqvist & Rowe, 2005), and complex feedback loops and correlations between them are predicted (Greenfield et al., 2014). Traditionally, sexual selection has been modelled under simplifying assumptions, and quantitative genetic approaches that avoided evolutionary dynamics have prevailed. New computing methods may be able to free the field from these constraints, and a trio of theoreticians (Chevalier, De Coligny & Labonne 2020) describe here a novel application of a ‘demo-genetic agent (or individual) based model’, a mouthful hereafter termed DG-ABM, for arriving at a holistic picture of the sexual selection trajectory. The application is built on the premise that traits, e.g. courtship, preference, gamete investment, competitiveness for mates, can influence the genetic architecture, e.g. correlations, of those traits. In turn, the genetic architecture can influence the expression and evolvability of the traits. Much of this influence occurs via demographic features, i.e. social environment, generated by behavioral interactions during sexual advertisement, courtship, mate guarding, parental care, post-mating dispersal, etc.
The authors provide a lengthy verbal description of their model, specifying the genomic and behavioral parameters that can be set and how a ‘run’ may be initialized. There is a link to an internet site where users can then enter their own parameter values and begin exploring hypotheses. Back in the article several simulations illustrate simple tests; e.g. how gamete investment and preference jointly evolve given certain survival costs. One obvious test would have been the preference – courtship genetic correlation that represents the core of Fisherian runaway selection, and it is regrettable that it was not examined under a range of demographic parameters. As presented the author’s DG-ABM appears particularly geared toward mating systems in ‘higher’ vertebrates, where couples form during a discrete mating season and are responsible for most reproduction. It is not clear how applicable the model could be to a full range of mating systems and nuances, including those in arthropods and other invertebrates as well as plants.
What is the likely value of the DG-ABM for sexual selection researchers? We will not be able to evaluate its potential impact until readers with specialized understanding of a question and taxon begin exploring and comparing their results with prior expectations. Of course, lack of congruence with earlier predictions would not invalidate the model. Hopefully, some of these specialists will have opportunities for comparing results with pertinent empirical data.

References

Ah-King, M. and Ahnesjo, I. 2013. The ‘sex role’ concept: An overview and evaluation Evolutionary Biology, 40, 461-470. doi: https://doi.org/10.1007/s11692-013-9226-7
Arnqvist, G. and Rowe, L. 2005. Sexual Conflict. Princeton University Press, Princeton. doi: https://doi.org/10.1515/9781400850600
Bell, G. 1982. The Masterpiece of Nature: The Evolution and Genetics of Sexuality. University of California Press, Berkeley.
Chevalier, L., De Coligny, F. and Labonne, J. (2020) A demogenetic individual based model for the evolution of traits and genome architecture under sexual selection. bioRxiv, 2020.04.01.014514, ver. 4 peer-reviewed and recommended by PCI Evol Biol. doi: https://doi.org/10.1101/2020.04.01.014514
Darwin, C. 1871. The Descent of Man and Selection in Relation to Sex. J. Murray, London.
Greenfield, M.D., Alem, S., Limousin, D. and Bailey, N.W. 2014. The dilemma of Fisherian sexual selection: Mate choice for indirect benefits despite rarity and overall weakness of trait-preference genetic correlation. Evolution, 68, 3524-3536. doi: https://doi.org/10.1111/evo.12542

A demogenetic agent based model for the evolution of traits and genome architecture under sexual selectionLouise Chevalier, François de Coligny, Jacques Labonne<p>Sexual selection has long been known to favor the evolution of mating behaviors such as mate preference and competitiveness, and to affect their genetic architecture, for instance by favoring genetic correlation between some traits. Reciprocall...Adaptation, Behavior & Social Evolution, Evolutionary Dynamics, Evolutionary Theory, Life History, Population Genetics / Genomics, Sexual SelectionMichael D Greenfield2020-04-02 14:44:25 View
31 Oct 2022
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Genotypic sex shapes maternal care in the African Pygmy mouse, Mus minutoides

Effect of sex chromosomes on mammalian behaviour: a case study in pygmy mice

Recommended by and ORCID_LOGO based on reviews by Marion Anne-Lise Picard, Caroline Hu and 1 anonymous reviewer

In mammals, it is well documented that sexual dimorphism and in particular sex differences in behaviour are fine-tuned by gonadal hormonal profiles. For example, in lemurs, where female social dominance is common, the level of testosterone in females is unusually high compared to that of other primate females (Petty and Drea 2015). 

Recent studies however suggest that gonadal hormones might not be the only biological factor involved in establishing sexual dimorphism, sex chromosomes might also play a role. The four core genotype (FCG) model and other similar systems allowing to decouple phenotypic and genotypic sex in mice have provided very convincing evidence of such a role (Gatewood et al. 2006; Arnold and Chen 2009; Arnold 2020a, 2020b). This however is a new field of research and the role of sex chromosomes in establishing sexually dimorphic behaviours has not been studied very much yet. Moreover, the FCG model has some limits. Sry, the male determinant gene on the mammalian Y chromosome might be involved in some sex differences in neuroanatomy, but Sry is always associated with maleness in the FCG model, and this potential role of Sry cannot be studied using this system.

Heitzmann et al. have used a natural system to approach these questions. They worked on the African Pygmy mouse, Mus minutoides, in which a modified X chromosome called X* can feminize X*Y individuals, which offers a great opportunity for elegant experiments on the effects of sex chromosomes versus hormones on behaviour. They focused on maternal care and compared pup retrieval, nest quality, and mother-pup interactions in XX, X*X and X*Y females. They found that X*Y females are significantly better at retrieving pups than other females. They are also much more aggressive towards the fathers than other females, preventing paternal care. They build nests of poorer quality but have similar interactions with pups compared to other females. Importantly, no significant differences were found between XX and X*X females for these traits, which points to an effect of the Y chromosome in explaining the differences between X*Y and other females (XX, X*X). Also, another work from the same group showed similar gonadal hormone levels in all the females (Veyrunes et al. 2022). 

Heitzmann et al. made a number of predictions based on what is known about the neuroanatomy of rodents which might explain such behaviours. Using cytology, they looked for differences in neuron numbers in the hypothalamus involved in the oxytocin, vasopressin and dopaminergic pathways in XX, X*X and X*Y females, but could not find any significant effects. However, this part of their work relied on very small sample sizes and they used virgin females instead of mothers for ethical reasons, which greatly limited the analysis. 

Interestingly, X*Y females have a higher reproductive performance than XX and X*X ones, which compensate for the cost of producing unviable YY embryos and certainly contribute to maintaining a high frequency of X* in many African pygmy mice populations (Saunders et al. 2014, 2022). X*Y females are probably solitary mothers contrary to other females, and Heitzmann et al. have uncovered a divergent female strategy in this species. Their work points out the role of sex chromosomes in establishing sex differences in behaviours. 

References

Arnold AP (2020a) Sexual differentiation of brain and other tissues: Five questions for the next 50 years. Hormones and Behavior, 120, 104691. https://doi.org/10.1016/j.yhbeh.2020.104691

Arnold AP (2020b) Four Core Genotypes and XY* mouse models: Update on impact on SABV research. Neuroscience & Biobehavioral Reviews, 119, 1–8. https://doi.org/10.1016/j.neubiorev.2020.09.021

Arnold AP, Chen X (2009) What does the “four core genotypes” mouse model tell us about sex differences in the brain and other tissues? Frontiers in Neuroendocrinology, 30, 1–9. https://doi.org/10.1016/j.yfrne.2008.11.001

Gatewood JD, Wills A, Shetty S, Xu J, Arnold AP, Burgoyne PS, Rissman EF (2006) Sex Chromosome Complement and Gonadal Sex Influence Aggressive and Parental Behaviors in Mice. Journal of Neuroscience, 26, 2335–2342. https://doi.org/10.1523/JNEUROSCI.3743-05.2006

Heitzmann LD, Challe M, Perez J, Castell L, Galibert E, Martin A, Valjent E, Veyrunes F (2022) Genotypic sex shapes maternal care in the African Pygmy mouse, Mus minutoides. bioRxiv, 2022.04.05.487174, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.04.05.487174

Petty JMA, Drea CM (2015) Female rule in lemurs is ancestral and hormonally mediated. Scientific Reports, 5, 9631. https://doi.org/10.1038/srep09631

Saunders PA, Perez J, Rahmoun M, Ronce O, Crochet P-A, Veyrunes F (2014) Xy Females Do Better Than the Xx in the African Pygmy Mouse, Mus Minutoides. Evolution, 68, 2119–2127. https://doi.org/10.1111/evo.12387

Saunders PA, Perez J, Ronce O, Veyrunes F (2022) Multiple sex chromosome drivers in a mammal with three sex chromosomes. Current Biology, 32, 2001-2010.e3. https://doi.org/10.1016/j.cub.2022.03.029

Veyrunes F, Perez J, Heitzmann L, Saunders PA, Givalois L (2022) Separating the effects of sex hormones and sex chromosomes on behavior in the African pygmy mouse Mus minutoides, a species with XY female sex reversal. bioRxiv, 2022.07.11.499546. https://doi.org/10.1101/2022.07.11.499546

Genotypic sex shapes maternal care in the African Pygmy mouse, Mus minutoidesLouise D Heitzmann, Marie Challe, Julie Perez, Laia Castell, Evelyne Galibert, Agnes Martin, Emmanuel Valjent, Frederic Veyrunes<p>Sexually dimorphic behaviours, such as parental care, have long been thought to be driven mostly, if not exclusively, by gonadal hormones. In the past two decades, a few studies have challenged this view, highlighting the direct influence of th...Behavior & Social Evolution, Evolutionary Ecology, Reproduction and SexGabriel Marais2022-04-08 20:09:58 View
17 Nov 2017
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ABC random forests for Bayesian parameter inference

Machine learning methods are useful for Approximate Bayesian Computation in evolution and ecology

Recommended by Michael Blum based on reviews by Dennis Prangle and Michael Blum

It is my pleasure to recommend the paper by Raynal et al. [1] about using random forest for parameter inference. There are two reviews about the paper, one review written by Dennis Prangle and another review written by myself. Both reviews were positive and included comments that have been addressed in the current version of the preprint.

The paper nicely shows that modern machine learning approaches are useful for Approximate Bayesian Computation (ABC) and more generally for simulation-driven parameter inference in ecology and evolution.

The authors propose to consider the random forest approach, proposed by Meinshausen [2] to perform quantile regression. The numerical implementation of ABC with random forest, available in the abcrf package, is based on the RANGER R package that provides a fast implementation of random forest for high-dimensional data.

According to my reading of the manuscript, there are 3 main advantages when using random forest (RF) for parameter inference with ABC. The first advantage is that RF can handle many summary statistics and that dimension reduction is not needed when using RF.

The second advantage is very nicely displayed in Figure 5, which shows the main result of the paper. If correct, 95% posterior credibility intervals (C.I.) should contain 95% of the parameter values used in simulations. Figure 5 shows that posterior C.I. obtained with rejection are too large compared to other methods. By contrast, C.I. obtained with regression methods have been shrunken. However, the shrinkage can be excessive for the smallest tolerance rates, with coverage values that can be equal to 85% instead of the expected 95% value. The attractive property of RF is that C.I. have been shrunken but the coverage is of 100% resulting in a conservative decision about parameter values.

The last advantage is that no hyperparameter should be chosen. It is a parameter free approach, which is desirable because of the potential difficulty of choosing an appropriate acceptance rate.

The main drawback of the proposed approach concerns joint parameter inference. There are many settings where the joint parameter distribution is of interest and the proposed RF approach cannot handle that. In population genetics for example, estimation of the severity and of the duration of the bottleneck should be estimated jointly because of identifiability issues. The challenge of performing joint parameter inference with RF might constitute a useful research perspective.
 

References
 

[1] Raynal L, Marin J-M, Pudlo P, Ribatet M, Robert CP, Estoup A. 2017. ABC random forests for Bayesian parameter inference. arXiv 1605.05537v4, https://arxiv.org/pdf/1605.05537
[2] Meinshausen N. 2006. Quantile regression forests. Journal of Machine Learning Research 7: 983-999. http://www.jmlr.org/papers/v7/meinshausen06a.html

ABC random forests for Bayesian parameter inferenceLouis Raynal, Jean-Michel Marin, Pierre Pudlo, Mathieu Ribatet, Christian P. Robert, Arnaud EstoupThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http:// dx.doi.org/ 10.24072/ pci.evolbiol.100036). Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian infer...Bioinformatics & Computational Biology, Evolutionary Applications, Other, Population Genetics / GenomicsMichael Blum 2017-07-06 07:42:00 View