Biological conservation aims at protecting the genetic diversity generated by evolutionary processes over the course of life's history on earth (Allendorf and Luikart 2007), and to be effective, it requires that its fundamental units (among which populations and species) be delimited as precisely as possible. This exercise is particularly important for corals because hybridisation and introgression have played a fundamental role in shaping their contemporary diversity (eg Veron 1995). 

In their review paper, Riginos et al (2024) show that 68% of nominal taxa investigated for genomic population structure bear the molecular signature of partial reproductive isolation, and can be considered as cryptic genetic groups. Another review study (published a day before the preprint of Riginos et al), converges in the finding that cryptic diversity is rampant in nominal coral species (Grupstra et al 2024). This result has strong bearing on the study of coral biology; as Riginos et al state, "any coral investigation that does not genotype the corals under study risks treating a heterogeneous mix of partially reproductively isolated taxa as a single species." The stakes are therefore high, given the ecological importance of corals and the ecosystem services they provide. 

While Grupstra et al (2024) discusses the impact of cryptic coral diversity in the context of functional differences in thermal adaptation and the processes that lead to cryptic lineages, Riginos et al (2024) provide a quantitative review of cryptic lineages within nominal species, providing reproducible criteria for delineation, details the importance of detecting hybrids, summarises how biodiversity metrics and conservation efforts can be biased by unrecognised cryptic lineages, offer recommendations on how to recognise and deal with cryptic diversity, and discuss how corals can be regarded as highly valuable model systems to study adaptation and speciation. The study of Riginos et al (2024) is therefore a must-read to all coral biologists, especially those involved in biological conservation.

References

Fred W. Allendorf  and Gordon Luikart (2007) Conservation and Genetics of Populations. Blackwell Publishing, Malden MA, USA.

Carsten G. B. Grupstra, Matías Gómez-Corrales, James E. Fifer, Hannah E. Aichelman, Kirstin S. Meyer-Kaiser, Carlos Prada, Sarah W. Davies (2024) Integrating cryptic diversity into coral evolution, symbiosis and conservation. Nat Ecol Evol 8, 622–636 (2024). https://doi.org/10.1038/s41559-023-02319-y

Cynthia Riginos, Iva Popovic, Zoe Meziere, Vhon Garcia, Ilha Byrne, Samantha Howitt, Hisatake Ishida, Kevin Bairos-Novak, Adriana Humanes, Hugo Scharfenstein, Thomas Richards, Ethan Briggs, Vanessa Clark, Chuan Lei, Mariam Khan, Katharine Prata (2024) Cryptic species and hybridisation in corals: challenges and opportunities for conservation and restoration. EcoEvoRxiv, ver.2 peer-reviewed and recommended by PCI Evol Biol https://doi.org/10.32942/X2502X

J. E. N. Veron (1995) Corals in Space and Time: The Biogeography and Evolution of the Scleractinia.  Cornell University Press

Insecticide resistance in mosquitoes represents a notable challenge to public health efforts aimed at controlling vector-borne diseases. Among mosquito species, Aedes aegypti is particularly significant due to its extensive geographic spread and its ability to transmit arboviruses causing diseases such as dengue, yellow fever, Zika, and chikungunya (Brown et al., 2014). Insecticide resistance typically develops through two main mechanisms: target-site mutations, which affect the insecticide's interaction with its target, and metabolic resistance, in which insecticide detoxification is enhanced in mosquitoes. While target-site mutations are well characterized, the mechanisms underlying metabolic resistance are understudied. 

The study by Bacot and colleagues (2024) contributes to our understanding of the genetic and evolutionary mechanisms driving insecticide resistance, focusing on a case of metabolic resistance in Aedes aegypti from French Guiana. Following the recent identification of a copy number variant region on chromosome 1, potentially linked to overexpression of detoxification enzymes (Cattel et al., 2020), this study explores the region’s genomic architecture, its likely origin and provides compelling evidence for its role in insecticide resistance.

Through RNA sequencing and whole-genome pool sequencing, the authors reveal that this 220 kilobase duplication increases the expression level of several clustered P450 genes. Cytochrome P450s are known to play a role in breaking down pyrethroids like deltamethrin, a commonly used insecticide. The role of P450 enzymes in detoxification was demonstrated by treating mosquitoes with piperonyl butoxide, a P450 enzyme inhibitor, and observing reduction in deltamethrin resistance, further confirmed by RNA interference experiments. Despite the clear advantages of this genomic duplication in conferring resistance, the study also uncovers a fitness cost associated with carrying the duplication. Through experimental evolution, the authors find that mosquitoes with the duplication experience reduced fitness in the absence of insecticide pressure. Given the regions structural complexity, the authors could not completely disassociate the effect of the duplicated region and that of a target-site mutation. However, they developed an assay that can accurately track the presence of this resistance allele in mosquito populations. 

Altogether, the study by Bacot et al. (2024) highlights the challenges of characterizing the phenotypic effect of copy number variant regions in complex genomes, such as that of Aedes aegypti. It emphasizes the need for further studies on the origin and spread of this duplication to better understand how similar resistance mechanisms might evolve and disseminate. Overall, the completeness and coherence of the narrative, the detailed and thorough analysis, and the insightful discussion, make this work not only a significant contribution to the field of insecticide resistance but an interesting read for the general evolutionary biology community.   

References

Brown, J. E., Evans, B. R., Zheng, W., Obas, V., Barrera-Martinez, L., Egizi, A., Zhao, H., Caccone, A., & Powell, J. R. (2014). Human impacts have shaped historical and recent evolution in Aedes aegypti, the dengue and yellow fever mosquito. Evolution, 68(2), 514–525. https://doi.org/10.1111/evo.12281

Cattel, J., Faucon, F., Le Péron, B., Sherpa, S., Monchal, M., Grillet, L., Gaude, T., Laporte, F., Dusfour, I., Reynaud, S., & David, J. P. (2019). Combining genetic crosses and pool targeted DNA-seq for untangling genomic variations associated with resistance to multiple insecticides in the mosquito Aedes aegypti. Evolutionary applications, 13(2), 303–317. https://doi.org/10.1111/eva.12867

Tiphaine Bacot, Chloe Haberkorn, Joseph Guilliet, Julien Cattel, Mary Kefi, Louis Nadalin, Jonathan Filee, Frederic Boyer, Thierry Gaude, Frederic Laporte, Jordan Tutagata, John Vontas, Isabelle Dusfour, Jean-Marc Bonneville, Jean-Philippe David (2024) A genomic duplication spanning multiple P450s contributes to insecticide resistance in the dengue mosquito Aedes aegypti. bioRxiv, ver.5 peer-reviewed and recommended by PCI Evol Biol https://doi.org/10.1101/2024.04.03.587871

Most flowering plants (almost 90% of species) are pollinated by animals (Ollerton et al. 2011). In fact, many plants are completely dependent on pollinator visits for reproductive success, due to the complete inability of selfing if they are self-incompatible or have strong gender differentiation, as in dioecious plants. Others have diminished reproductive output in the absence of pollinators, even being self-compatible, if their flowers present strong herkogamy or dichogamy, making autonomous selfing more difficult. Ultimately, all animal-pollinated plant species rely on pollinators for outcrossing. Depending on the genetic structure of plant populations and the movement patterns of these animals, outcrossing patterns will shape the population genetic variation, which will determine its adaptive fate. Thus, understanding the mechanisms governing the pollination interaction is crucial for unraveling the uncertainties of a huge proportion of biodiversity on Earth. Being mutualistic by definition, the animal side of this interaction is less understood, despite most pollinator groups being likely dependent on it for their persistence and perhaps diversity (Ollerton 2017). The role of pollinators in plant diversification has generated much literature and controversy ever since Darwin and his “abominable mystery” about angiosperm diversification (Friedman 2009). However, the other way around, that of plant`s effect on pollinator diversification, is more debatable. A remarkable example of this effect is the possible case of co-speciation mediated by nursery (brood site) pollination, which also includes antagonistic insect herbivory (Wiens et al. 2015), as in some Silene species and their moth pollinators and herbivores (Hembry and Althoff 2016).
 
A properly functional pollination interaction relies on efficient pollinators being attracted to flowers (by visual and olfactory stimuli), rewarded or deceived by them (in feeding, nesting, basking, mating, etc. sites), fit the flower shape and contact the sex organs to enhance both male and female plant fitness. Whereas flower rewards, visually attractive stimuli, and flower architecture and shape greatly dominate pollination studies; there are much fewer studies of olfactory attractive stimuli through flower volatile organic compounds (VOC), due to inherent methodological difficulties (Raguso 2008). Most of the studies dealing with flower volatiles are correlative by nature, whereas manipulative experimental approaches are far less common. 
 
Albeit still plant-centered, the manuscript by Barbot et al. (2024) on Silene dioica and its varied pollinator arrays has great merit in including many of the issues mentioned above to solve long-standing questions in plant reproduction. It elegantly fills a gap with well-designed and performed experiments in a particular pollination mode, nursery pollination, which is now considered more frequent and diverse than formerly thought (Nunes et al. 2018, Haran et al. 2023, Suetsugu 2023). The authors demonstrate that Silene dioica has a truly mixed pollination system, including not only generalist diurnal pollinators as it was formerly considered but also nocturnal pollinators of similar proven efficiency. Although the specialized nursery pollination system of Silene-Hadena is widely reported and described in the literature (Kephart et al. 2006; Prieto-Benítez et al. 2017), it was not formerly considered important for Silene dioica, based on its floral syndrome. However, the experiments designed by Barbot et al. (2024) explore in detail the mechanisms of attraction of nocturnal pollinators and their consequences for plant reproductive success, fully confirming the proper functioning of nursery pollination in this plant species. All these prospects are robustly performed through classical sound phenotypic selection analyses and manipulative experiments, together with other approaches less frequent due to technical difficulties but critical when testing authors’ hypotheses. In particular, male fitness estimates using suitable microsatellite markers are especially appropriate in this dioecious species, although they are also very useful in hermaphroditic species when different pollinators and flower variants are interacting (Kulbaba and Worley 2013, Simón-Porcar et al. 2015). Finally, the manipulation of flower fragrance (in fact, of a single VOC) has proved also critical to getting insight into its effect on night pollinators and their joint role as ovipositors and thus predators. All these questions are addressed with a fully crossed experimental design that allows unveiling interactions between experimental factors, a challenge in experimental biology, especially under natural conditions. 
 
In evolutionary biology, most experiments are carried out in laboratories, where factors under scrutiny are carefully controlled and hence their effects are easy to reproduce. The cost of this approach is that the variables of interest are oversimplified and difficult to extrapolate to real ecological conditions. In evolutionary ecology, experiments under field conditions greatly solve this shortcoming, but the cost arises in the difficulties of dealing with several interacting and uncontrolled factors. The study by Barbot et al. (2024) nicely addresses real-world questions in a specialized pollination plus herbivory interaction. The results are robust and pave the road for further overarching pursuits, as mentioned by the reviewers. Thus, it would be interesting to assess actual, absolute values of pollen dispersal distance in natural populations, the selection exerted through the complete reproductive period of male and female plants, provided that they are different, or the effect of using more natural flower bouquets, in the next steps. However, as it stands, this outstanding study will be of high interest to scholars on any of the many topics dealt with there, but also to students willing to start research in the fascinating field of experimental pollination biology, given the wide array of questions addressed and the modern methodological approaches provided.
 
Acknowledgments

The authors of this recommendation benefitted from grants provided by grants PID2021-122715NB-I00 and TED2021-131037B-I00 funded by MCIN/AEI/ 10.13039/501100011033 and by the “European Union NextGeneration EU/PRTR”, and by MSCA-IF-2019-89789.
 
References

Barbot, E., Dufaÿ, M., Godé, C., & De Cauwer, I. (2024). Exploring the effect of scent emission and exposition to diurnal versus nocturnal pollinators on selection patterns on floral traits. Zenodo. https://doi.org/10.5281/zenodo.11490231

Friedman, W. E. (2009). The meaning of Darwin's “abominable mystery”. American Journal of Botany, 96(1), 5-21. https://doi.org/10.3732/ajb.0800150

Haran, J., Kergoat, G. J., & de Medeiros, B. A. (2023). Most diverse, most neglected: weevils (Coleoptera: Curculionoidea) are ubiquitous specialized brood-site pollinators of tropical flora. Peer Community Journal, 3. https://doi.org/10.24072/pcjournal.279 

Hembry, D.H. and Althoff, D.M. (2016), Diversification and coevolution in brood pollination mutualisms: Windows into the role of biotic interactions in generating biological diversity. American Journal of Botany, 103: 1783-1792. https://doi.org/10.3732/ajb.1600056

Kephart, S., Reynolds, R. J., Rutter, M. T., Fenster, C. B., & Dudash, M. R. (2006). Pollination and seed predation by moths on Silene and allied Caryophyllaceae: evaluating a model system to study the evolution of mutualisms. New Phytologist, 169(4), 667-680. https://doi.org/10.1111/j.1469-8137.2005.01619.x

Kulbaba, M. W., & Worley, A. C. (2013). Selection on Polemonium brandegeei (Polemoniaceae) flowers under hummingbird pollination: in opposition, parallel, or independent of selection by hawkmoths?. Evolution, 67(8), 2194-2206. https://doi.org/10.1111/evo.12102

Nunes, C. E. P., Maruyama, P. K., Azevedo-Silva, M., & Sazima, M. (2018). Parasitoids turn herbivores into mutualists in a nursery system involving active pollination. Current Biology, 28(6), 980-986. https://doi.org/10.1016/j.cub.2018.02.013

Ollerton, J. (2017). Pollinator diversity: distribution, ecological function, and conservation. Annual review of ecology, evolution, and systematics, 48(1), 353-376. https://doi.org/10.1146/annurev-ecolsys-110316-022919

Ollerton, J., Winfree, R., & Tarrant, S. (2011). How many flowering plants are pollinated by animals?. Oikos, 120(3), 321-326. https://doi.org/10.1111/j.1600-0706.2010.18644.x

Prieto-Benitez, S., Yela, J. L., & Gimenez-Benavides, L. (2017). Ten years of progress in the study of Hadena-Caryophyllaceae nursery pollination. A review in light of new Mediterranean data. Flora, 232, 63-72. https://doi.org/10.1016/j.flora.2017.02.004

Raguso, R. A. (2008). Wake up and smell the roses: the ecology and evolution of floral scent. Annual review of ecology, evolution, and systematics, 39(1), 549-569. https://doi.org/10.1146/annurev.ecolsys.38.091206.095601

Simón-Porcar, V. I., Meagher, T. R., & Arroyo, J. (2015). Disassortative mating prevails in style-dimorphic Narcissus papyraceus despite low reciprocity and compatibility of morphs. Evolution, 69(9), 2276-2288. https://doi.org/10.1111/evo.12731

Suetsugu, K. (2023). A novel nursery pollination system between a mycoheterotrophic orchid and mushroom-feeding flies. Ecology, 104(11), e4152. https://doi.org/10.1002/ecy.4152

Wiens, J. J., Lapoint, R. T., & Whiteman, N. K. (2015). Herbivory increases diversification across insect clades. Nature communications, 6(1), 8370. https://doi.org/10.1038/ncomms9370 

The study by Pfenninger (2025) addresses the critical need to understand the genomic basis of ecologically important traits to better predict and respond to the impacts of global change on biodiversity (Gienapp et al. 2017). It introduces the popGWAS, a novel GWAS approach, which utilizes phenotypic population means and genome-wide allele frequency data, obtainable through methods like Pool-sequencing (Pool-Seq), to identify the genetic loci underlying quantitative polygenic traits in natural populations and predict their mean. The core idea is that trait-increasing alleles should exhibit higher frequencies in populations with higher mean trait values. popGWAS then maps mean allele frequencies across populations to their trait means. Working with as many allele frequency values as populations sampled, popGWAS potentially has more power to find significant associations at genomic loci than individual-based GWAS working with three genotypes at a locus. This new method addresses some of the problems faced by traditional genome-wide association studies (GWAS), which require extensive resources and large sample sizes, posing challenges for biodiversity research on non-model species in natural populations. 

To evaluate the effectiveness of popGWAS, Pfenninger (2025) conducted extensive population genetic forward simulations, examining scenarios with varying numbers of populations, ranging from 12 to 60. The results indicated that popGWAS performance improved with increasing sample size, showing a diminishing return above 36 populations. In a direct comparison across all simulation scenarios, popGWAS consistently outperformed individual-based GWAS (iGWAS). On average, popGWAS identified more true positive loci than iGWAS. In addition, when combined with minimum entropy feature selection (MEFS), popGWAS achieved large predictive accuracy of population means of 0.8 or better in over 97% of simulations with 36 or more populations, regardless of other parameters. In contrast, iGWAS failed to generate valid phenotypic predictions in over 70% of the simulations. Also, unlike iGWAS, popGWAS did not suffer from p-value inflation. Yet, population structure or varying levels of relatedness among individuals were not fully accounted for in the simulations. The extent to which popGWAS would be sensitive to such individual covariates remains to be shown. Finally, popGWAS was relatively insensitive to low trait heritability because random individual variation gets averaged out when calculating the population mean trait value. 

The study demonstrates that popGWAS is a promising approach, particularly for oligogenic and moderately polygenic traits. The method performs more poorly for polygenic traits with large genetic redundancy, where different alleles contribute to the same trait mean in different populations. The method thus performs better when large-effect loci contribute to genetic differentiation in parallel across populations, as expected when gene flow is moderate to high (Yeaman & Whitlock 2011). Low genomic predictability is reached when drift dominates or when genetic architectures are highly polygenic.

The popGWAS method proved effective with a moderate number of sampled populations and, when combined with machine learning for genomic prediction, exhibited strong performance in predicting population means, even for low-heritability traits. Notably, popGWAS consistently outperformed iGWAS in terms of identifying true positive loci and prediction accuracy. This suggests that popGWAS can make GWAS studies more accessible for biodiversity genomics research, providing a valuable tool for dissecting the genetic basis of complex traits in natural populations. A key aspect contributing to the efficiency of popGWAS is its compatibility with pooled sequencing (Pool-Seq). Pool-Seq provides estimates of allele frequencies within a population by sequencing a mixed DNA sample representing multiple individuals from that population (Futschik & Schlötterer 2010). This approach is significantly more cost-effective than sequencing each individual separately, allowing researchers to obtain genome-wide allele frequency data across multiple populations with a substantially reduced budget. This data efficiency makes GWAS more accessible to a wider range of researchers, particularly those working in biodiversity genomics where financial resources may be limited. Furthermore, popGWAS can be coupled with bulk phenotyping methods, such as automatic video recording, remote sensing, metabolomics/transcriptomics, etc., to efficiently obtain population-level phenotypic data, further streamlining the research process. Ultimately, popGWAS represents a valuable addition to the geneticist's toolkit, offering a complementary approach to iGWAS that can be particularly advantageous in specific research contexts where predicting trait mean is more important than resolving the precise genetic basis of a trait.

References

Futschik, A. and Schlötterer, C. 2010. The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples. Genetics 186(1): 207-218. https://doi.org/10.1534/genetics.110.114397

Gienapp, P., Fior, S., Guillaume, F., Lasky, J. R., Sork, V. L. and Csilléry, K. 2017. Genomic Quantitative Genetics to Study Evolution in the Wild. Trends Ecol. Evol. 32(12): 897-908. https://doi.org/10.1016/j.tree.2017.09.004

Markus Pfenninger (2025) On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS). bioRxiv, ver.3 peer-reviewed and recommended by PCI Evol Biol https://doi.org/10.1101/2024.06.12.598621

Yeaman, S. and Whitlock, M. C. 2011. The genetic architecture of adaptation under migration-selection balance. Evolution 65(7): 1897-1911. https://doi.org/10.1111/j.1558-5646.2011.01269.x

We live both in a worrying and fascinating time. Worrying because human-induced global change has dramatic consequences on biodiversity around the world. Fascinating because these changes enable us to witness evolutionary processes unfolding on relatively short time scales. One such process is biological invasion. An intriguing evolutionary question is to understand which factor facilitates the success of an invasive species. In particular, serial bottlenecks at the expanding front should reduce the effective population size and decrease genetic diversity. Theoretically, this will increase the fixation of deleterious mutations due to the effect of genetic drift and overall affect the evolutionary potential of the invading species. In the short term, reduced genetic diversity and inbreeding in small populations increases the number of recessive deleterious variants exposed in a homozygous state. This may generate a reduction in mean fitness of the population. However, in the long term and under specific demographic scenarios recessive deleterious alleles may be more efficiently removed by purifying selection. Such purging may explain the success of invasion by reducing inbreeding depression and minimizing loss of fitness. Here, Lombaert et al. estimate the genetic load in two invasive insect species, a predator species, the harlequin ladybird (Harmonia axyridis) and a crop pest species, the western corn rootworm (Diabrotica virgifera virgifera). 

The authors smartly took advantage of a pool-seq transcriptome-based exome capture method to estimate genetic load and assess the purge hypothesis using standard population genetic statistics, such as the ratio of nonsynonymous over synonymous expected heterozygosity, the frequency of derived alleles, and their excess or deficit.

The results revealed different patterns in the two species:

In the western corn rootworm, the authors find a clear signal of reduced genetic diversity in invasive populations. This was associated with a slightly reduced genetic load. However, there was only marginal evidence of purging regarding the most deleterious mutations, and in a single population, with moderately deleterious variants being weakly purged, as theoretically expected. 

In the harlequin ladybird, in contrast, the reduction of genetic diversity in invasive populations has been small, a result related to the mild severity of the bottlenecks. In this species, the authors found a tendency toward fixation of the genetic load and no signal of purging. 

Such results are intriguing, showing that different species seem to exhibit contrasted fate of genetic load. Differences in the invasion history and ecology of the species may explain these patterns. This is one of the first studies to use a population genomics approach to study the genetic load associated with biological invasion. Future studies based on whole genome data collected at the individual level across multiple species are needed to better understand the dynamics of genetic load during biological invasion and to draw more general conclusions. Advances in forward simulations may also be used to shed light on the evolution of the genetic load at different stages of the invasion process and under different strengths of bottlenecks.

References

Eric Lombaert, Aurelie Blin, Barbara Porro, Thomas Guillemaud, Julio S Bernal, Gary Chang, Natalia Kirichenko, Thomas W Sappington, Stefan Toepfer, Emeline Deleury (2025) Unraveling genetic load dynamics during biological invasion: insights from two invasive insect species. bioRxiv, ver.3 peer-reviewed and recommended by PCI Evol Biol https://doi.org/10.1101/2024.09.02.610743