Latest recommendations
Id | Title * | Authors * | Abstract * | Picture * | Thematic fields * | Recommender▲ | Reviewers | Submission date | |
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13 Dec 2018
![]() A behavior-manipulating virus relative as a source of adaptive genes for parasitoid waspsD. Di Giovanni, D. Lepetit, M. Boulesteix, M. Ravallec, J. Varaldi https://doi.org/10.1101/342758Genetic intimacy of filamentous viruses and endoparasitoid waspsRecommended by Ignacio BravoViruses establish intimate relationships with the cells they infect. The virocell is a novel entity, different from the original host cell and beyond the mere combination of viral and cellular genetic material. In these close encounters, viral and cellular genomes often hybridise, combine, recombine, merge and excise. Such chemical promiscuity leaves genomics scars that can be passed on to descent, in the form of deletions or duplications and, importantly, insertions and back and forth exchange of genetic material between viruses and their hosts. References [1] Di Giovanni, D., Lepetit, D., Boulesteix, M., Ravallec, M., & Varaldi, J. (2018). A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps. bioRxiv, 342758, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/342758 | A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps | D. Di Giovanni, D. Lepetit, M. Boulesteix, M. Ravallec, J. Varaldi | <p>To circumvent host immune response, numerous hymenopteran endo-parasitoid species produce virus-like structures in their reproductive apparatus that are injected into the host together with the eggs. These viral-like structures are absolutely n... | ![]() | Adaptation, Behavior & Social Evolution, Genetic conflicts, Genome Evolution | Ignacio Bravo | 2018-07-18 15:59:14 | View | |
26 Oct 2021
![]() Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North AfricaOlvera-Vazquez S.G., Remoué C., Venon A, Rousselet A., Grandcolas O., Azrine M., Momont L., Galan M., Benoit L., David G., Alhmedi A., Beliën T., Alins G., Franck P., Haddioui A., Jacobsen S.K., Andreev R., Simon S., Sigsgaard L., Guibert E., Tournant L., Gazel F., Mody K., Khachtib Y., Roman A., Ursu T.M., Zakharov I.A., Belcram H., Harry M., Roth M., Simon J.C., Oram S., Ricard J.M., Agnello A., Beers E. H., Engelman J., Balti I., Salhi-Hannachi A., Zhang H., Tu H., Mottet C., Barrès B., Degra... https://doi.org/10.1101/2020.12.11.421644The evolutionary puzzle of the host-parasite-endosymbiont Russian doll for apples and aphidsRecommended by Ignacio BravoEach individual multicellular organism, each of our bodies, is a small universe. Every living surface -skin, cuticle, bark, mucosa- is the home place to milliards of bacteria, fungi and viruses. They constitute our microbiota. Some of them are essential for certain organisms. Other could not live without their hosts. For many species, the relationship between host and microbiota is so close that their histories are inseparable. The recognition of this biological inextricability has led to the notion of holobiont as the organism ensemble of host and microbiota. When individuals of a particular animal or plant species expand their geographical range, it is the holobiont that expands. And these processes of migration, expansion and colonization are often accompanied by evolutionary and ecological innovations in the interspecies relationships, at the macroscopic level (e.g. novel predator-prey or host-parasite interactions) and at the microscopic level (e.g. changes in the microbiota composition). From the human point of view, these novel interactions can be economically disastrous if they involve and threaten important crop or cattle species. And this is especially worrying in the present context of genetic standardization and intensification for mass-production on the one hand, and of climate change on the other. With this perspective, the international team led by Amandine Cornille presents a study aiming at understanding the evolutionary history of the rosy apple aphid Dysaphis plantaginea Passerini, a major pest of the cultivated apple tree Malus domestica Borkh (1). The apple tree was probably domesticated in Central Asia, and later disseminated by humans over the world in different waves, and it was probably introduced in Europe by the Greeks. It is however unclear when and where D. plantaginea started parasitizing the cultivated apple tree. The ancestral D. plantaginea could have already infected the wild ancestor of current cultivated apple trees, but the aphid is not common in Central Asia. Alternatively, it may have gained access only later to the plant, possibly via a host jump, from Pyrus to Malus that may have occurred in Asia Minor or in the Caucasus. In the present preprint, Olvera-Vázquez and coworkers have analysed over 650 D. plantaginea colonies from 52 orchards in 13 countries, in Western, Central and Eastern Europe as well as in Morocco and the USA. The authors have analysed the genetic diversity in the sampled aphids, and have characterized as well the composition of the associated endosymbiont bacteria. The analyses detect substantial recent admixture, but allow to identify aphid subpopulations slightly but significantly differentiated and isolated by distance, especially those in Morocco and the USA, as well as to determine the presence of significant gene flow. This process of colonization associated to gene flow is most likely indirectly driven by human interactions. Very interestingly, the data show that this genetic diversity in the aphids is not reflected by a corresponding diversity in the associated microbiota, largely dominated by a few Buchnera aphidicola variants. In order to determine polarity in the evolutionary history of the aphid-tree association, the authors have applied approximate Bayesian computing and machine learning approaches. Albeit promising, the results are not sufficiently robust to assess directionality nor to confidently assess the origin of the crop pest. Despite the large effort here communicated, the authors point to the lack of sufficient data (in terms of aphid isolates), especially originating from Central Asia. Such increased sampling will need to be implemented in the future in order to elucidate not only the origin and the demographic history of the interaction between the cultivated apple tree and the rosy apple aphid. This knowledge is needed to understand how this crop pest struggles with the different seasonal and geographical selection pressures while maintaining high genetic diversity, conspicuous gene flow, differentiated populations and low endosymbiontic diversity. References
| Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa | Olvera-Vazquez S.G., Remoué C., Venon A, Rousselet A., Grandcolas O., Azrine M., Momont L., Galan M., Benoit L., David G., Alhmedi A., Beliën T., Alins G., Franck P., Haddioui A., Jacobsen S.K., Andreev R., Simon S., Sigsgaard L., Guibert E., Tour... | <p style="text-align: justify;">With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insec... | ![]() | Phylogeography & Biogeography, Population Genetics / Genomics, Species interactions | Ignacio Bravo | 2020-12-11 19:22:54 | View | |
25 Sep 2023
![]() Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoansFlorian Benitiere, Anamaria Necsulea, Laurent Duret https://doi.org/10.1101/2022.12.09.519597The drift barrier hypothesis and the limits to alternative splicing accuracyRecommended by Ignacio BravoAccurate information flow is central to living systems. The continuity of genomes through generations as well as the reproducible functioning and survival of the individual organisms require a faithful information transfer during replication, transcription and translation. The differential efficiency of natural selection against “mistakes” results in decreasing fidelity rates for replication, transcription and translation. At each level in the information flow chain (replication, transcription, translation), numerous complex molecular systems have evolved and been selected for preventing, identifying and, when possible, correcting or removing such “mistakes” arising during information transfer. However, fidelity cannot be improved ad infinitum. First, because of the limits imposed by the physical nature of the processes of copying and recoding information over different molecular supports: all mechanisms ensuring fidelity during biological information transfer ultimately rely on chemical kinetics and thermodynamics. The more accurate a copying process is, the lower the synthesis rate and the higher the energetic cost of correcting errors. Second, because of the limits imposed by random genetic drift: natural selection cannot effectively act on an allele that contributes with a small differential advantage unless effective population size is large. If s <1/Ne (or s <1/(2Ne) in diploids) the allele frequency in the population is de facto subject to neutral drift processes. In their preprint “Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans”, Bénitière, Necsulea and Duret explore the validity of this last mentioned “drift barrier” hypothesis for the case study of alternative splicing diversity in eukaryotes (Bénitière et al. 2022). Splicing refers to an ensemble of eukaryotic molecular processes mediated by a large number of proteins and ribonucleoproteins and involving nucleotide sequence recognition, that uses as a molecular substrate a precursor messenger RNA (mRNA), directly transcribed from the DNA, and produces a mature mRNA by removing introns and joining exons (Chow et al. 1977). Alternative splicing refers to the case in which different molecular species of mature mRNAs can be produced, either by cis-splicing processes acting on the same precursor mRNA, e.g. by varying the presence/absence of different exons or by varying the exon-exon boundaries, or by trans-splicing processes, joining exons from different precursor mRNA molecules. The diversity of mRNA molecular species generated by alternative splicing enlarges the molecular phenotypic space that can be generated from the same genotype. In humans, alternative splicing occurs in around 95% of the ca. 20,000 genes, resulting in ca. 100,000 medium-to-high abundance transcripts (Pan et al. 2008). In multicellular organisms, the frequency of alternatively spliced mRNAs varies between tissues and across ontogeny, often in a switch-like pattern (Wang et al. 2008). In the molecular and cell biology community, it is commonly accepted that splice variants contribute with specific functions (Marasco and Kornblihtt 2023) although there exists a discussion around the functional nature of low-frequency splice variants (see for instance the debate between Tress et al. 2017 and Blencowe 2017). The origin, diversity, regulation and evolutionary advantage of alternative splicing constitutes thus a playground of the selectionist-neutralist debate, with one extreme considering that most splice variants are mere “mistakes” of the splicing process (Pickrell et al. 2010), and the other extreme considering that alternative splicing is at the core of complexity in multicellular organisms, as it increases the genome coding potential and allows for a large repertoire of cell types (Chen et al. 2014). In their manuscript, Bénitière, Necsulea and Duret set the cursor towards the neutralist end of the gradient and test the hypothesis of whether the high alternative splice rate in “complex” organisms corresponds to a high rate of splicing “mistakes”, arising from the limit imposed by the drift barrier effect on the power of natural selection to increase accuracy (Bush et al. 2017). In their preprint, the authors convincingly show that in metazoans a fraction of the variation of alternative splicing rate is explained by variation in proxies of population size, so that species with smaller Ne display higher alternative splice rates. They communicate further that abundant splice variants tend to preserve the reading frame more often than low-frequency splice variants, and that the nucleotide splice signals in abundant splice variants display stronger evidence of purifying selection than those in low-frequency splice variants. From all the evidence presented in the manuscript, the authors interpret that “variation in alternative splicing rate is entirely driven by variation in the efficacy of selection against splicing errors”. The authors honestly present some of the limitations of the data used for the analyses, regarding i) the quality of the proxies used for Ne (i.e. body length, longevity and dN/dS ratio); ii) the heterogeneous nature of the RNA sequencing datasets (full organisms, organs or tissues; different life stages, sexes or conditions); and iii) mostly short RNA reads that do not fully span individual introns. Further, data from bacteria do not verify the herein communicated trends, as it has been shown that bacterial species with low population sizes do not display higher transcription error rates (Traverse and Ochman 2016). Finally, it will be extremely interesting to introduce a larger evolutionary perspective on alternative splicing rates encompassing unicellular eukaryotes, in which an intriguing interplay between alternative splicing and gene duplication has been communicated (Hurtig et al. 2020). The manuscript from Bénitière, Necsulea and Duret makes a significant advance to our understanding of the diversity, the origin and the physiology of post-transcriptional and post-translational mechanisms by emphasising the fundamental role of non-adaptive evolutionary processes and the upper limits to splicing accuracy set by genetic drift. References Bénitière F, Necsulea A, Duret L. 2023. Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.12.09.519597 Blencowe BJ. 2017. The Relationship between Alternative Splicing and Proteomic Complexity. Trends Biochem Sci 42:407–408. https://doi.org/10.1016/j.tibs.2017.04.001 Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. 2017. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci 372:20150474. https://doi.org/10.1098/rstb.2015.0474 Chen L, Bush SJ, Tovar-Corona JM, Castillo-Morales A, Urrutia AO. 2014. Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. Mol Biol Evol 31:1402–1413. https://doi.org/10.1093/molbev/msu083 Chow LT, Gelinas RE, Broker TR, Roberts RJ. 1977. An amazing sequence arrangement at the 5’ ends of adenovirus 2 messenger RNA. Cell 12:1–8. https://doi.org/10.1016/0092-8674(77)90180-5 Hurtig JE, Kim M, Orlando-Coronel LJ, Ewan J, Foreman M, Notice L-A, Steiger MA, van Hoof A. 2020. Origin, conservation, and loss of alternative splicing events that diversify the proteome in Saccharomycotina budding yeasts. RNA 26:1464–1480. https://doi.org/10.1261/rna.075655.120 Marasco LE, Kornblihtt AR. 2023. The physiology of alternative splicing. Nat Rev Mol Cell Biol 24:242–254. https://doi.org/10.1038/s41580-022-00545-z Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415. https://doi.org/10.1038/ng.259 Pickrell JK, Pai AA, Gilad Y, Pritchard JK. 2010. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet 6:e1001236. https://doi.org/10.1371/journal.pgen.1001236 Traverse CC, Ochman H. 2016. Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles. Proc Natl Acad Sci U S A 113:3311–3316. https://doi.org/10.1073/pnas.1525329113 Tress ML, Abascal F, Valencia A. 2017. Alternative Splicing May Not Be the Key to Proteome Complexity. Trends Biochem Sci 42:98–110. https://doi.org/10.1016/j.tibs.2016.08.008 Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476. https://doi.org/10.1038/nature07509 | Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans | Florian Benitiere, Anamaria Necsulea, Laurent Duret | <p style="text-align: justify;">Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the nu... | ![]() | Bioinformatics & Computational Biology, Genome Evolution, Molecular Evolution, Population Genetics / Genomics | Ignacio Bravo | Anonymous | 2022-12-12 14:00:01 | View |
11 Oct 2022
![]() The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol ProductionWarren R Francis https://doi.org/10.20944/preprints202004.0186.v5Gene family analysis suggests new evolutionary scenario for sterol and hopanoid biomarkersRecommended by Iker Irisarri based on reviews by Samuel Abalde, Denis Baurain and Jose Ramon Pardos-BlasSterols and hopanoids are sometimes used as biomarkers to infer the origin of certain groups of organisms. Traditionally, hopanoid-derived products in ancient rocks have been considered to indicate the presence of bacteria, whereas sterol derivatives have been considered to be exclusive to eukaryotes. However, a closer look at the topic reveals a rather complex distribution of either compound in both bacteria and eukaryotes. (1). The known biosynthetic pathways for sterols and hopanoids are similar but diverge at a critical step where two different enzymes are used: squalene-hopene cyclase (SHC) and oxidosqualene cyclase (OSC), the latter requiring oxygen. These two enzymes belong to the same gene family, whose complex evolutionary history is difficult to reconcile with the known species phylogeny. In this study (2), Dr. Warren R. Francis revisits the evolution of this gene family using an extended dataset with a broader taxonomic representation. In contrast to the traditional representation of the tree rooted between SHC and OSC paralogs (i.e., based on function), the author proposes that rooting the tree within bacterial SHCs and assuming a secondary origin of OSC is more parsimonious. This postulates SHC to be the ancestral function –retained in many extant bacteria and some eukaryotes– and OSC to have emerged later within bacteria –currently being mostly present in eukaryotes–. The reconstructed evolutionary history is arguably complex and can only be reconciled with the species' phylogeny by invoking many secondary losses. These losses are considered likely because many extant species acquire sterols and hopanoids by diet and lack one or both enzymes. Some cases of recent horizontal gene transfer are also proposed. In contrast to the dichotomy between bacterial SHCs and eukaryote OSCs, the new proposed scenario suggests that the eukaryote ancestor likely inherited both enzymes from bacteria and thus could be able to synthesize both sterols and hopanoids. Under this hypothesis, not only bacteria but also eukaryotes could be responsible for the hopane found in old rocks. This agrees with eukaryote fossils dating back to more than 1 billion years ago (3). Also, the observed increase of sterane levels in rocks ~600-700 million years old cannot be associated with the origin of eukaryotes, which is a much older event, but could rather reflect changes in atmospheric oxygen levels because oxygen is required for the synthesis of sterols by OSC. References 1. Santana-Molina C, Rivas-Marin E, Rojas AM, Devos DP (2020) Origin and Evolution of Polycyclic Triterpene Synthesis. Molecular Biology and Evolution, 37, 1925–1941. https://doi.org/10.1093/molbev/msaa054 2. Francis WR (2022) The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol Production. Preprints, 2020040186, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.20944/preprints202004.0186.v5 3. Butterfield NJ (2000) Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology, 26, 386–404. https://doi.org/10.1666/0094-8373(2000)026<0386:BPNGNS>2.0.CO;2 | The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol Production | Warren R Francis | <p>Steroid and hopanoid biomarkers can be found in ancient rocks and may give a glimpse of what life was present at that time. Sterols and hopanoids are produced by two related enzymes, though the evolutionary history of this protein family is com... | ![]() | Bioinformatics & Computational Biology, Evolutionary Ecology, Molecular Evolution, Paleontology, Phylogenetics / Phylogenomics | Iker Irisarri | 2021-01-13 16:03:29 | View | |
05 Aug 2020
Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognitaDjampa KL Kozlowski, Rahim Hassanaly-Goulamhoussen, Martine Da Rocha, Georgios D Koutsovoulos, Marc Bailly-Bechet, Etienne GJ Danchin https://doi.org/10.1101/2020.04.30.069948DNA transposons drive genome evolution of the root-knot nematode Meloidogyne incognitaRecommended by Ines AlvarezDuplications, mutations and recombination may be considered the main sources of genomic variation and evolution. In addition, sexual recombination is essential in purging deleterious mutations and allowing advantageous allelic combinations to occur (Glémin et al. 2019). However, in parthenogenetic asexual organisms, variation cannot be explained by sexual recombination, and other mechanisms must account for it. Although it is known that transposable elements (TE) may influence on genome structure and gene expression patterns, their role as a primary source of genomic variation and rapid adaptability has received less attention. An important role of TE on adaptive genome evolution has been documented for fungal phytopathogens (Faino et al. 2016), suggesting that TE activity might explain the evolutionary dynamics of this type of organisms. References [1] Bessereau J-L. 2006. Transposons in C. elegans. WormBook. 10.1895/wormbook.1.70.1 | Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita | Djampa KL Kozlowski, Rahim Hassanaly-Goulamhoussen, Martine Da Rocha, Georgios D Koutsovoulos, Marc Bailly-Bechet, Etienne GJ Danchin | <p>Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant ... | Adaptation, Bioinformatics & Computational Biology, Genome Evolution, Molecular Evolution, Population Genetics / Genomics, Reproduction and Sex | Ines Alvarez | 2020-05-04 11:43:14 | View | ||
26 Aug 2024
![]() Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western EuropeSolenn Stoeckel, Ronan Becheler, Luis Portillo-Lemus, Marilyne Harang, Anne-Laure Besnard, Gilles Lassalle, Romain Causse-Védrines, Sophie Michon-Coudouel, Daniel J. Park, Bernard J. Pope, Eric J. Petit, Dominique Barloy https://doi.org/10.1101/2024.03.21.586104Mixed reproduction modes explain a high genetic diversity in the invasive plant Ludwigia grandiflora subsp. hexapetala in western EuropeRecommended by Ines AlvarezThe introduction of Ludwigia species as ornamental plants in both North America and Europe dates back almost two centuries, during which time they expanded as naturalized and later invasive species in these territories (Dandelot et al. 2005, Okada et al. 2009). Repeated deliberate or non-deliberate introductions over time of this species complex that can hybridize has given rise to an evolutionarily complex scenario, which is compounded by the difficulty in delimiting some of these species and by the diversity of their modes of reproduction. Dandelot (2004) and Dandelot et al. (2005) determined the presence of two Ludwigia taxa in France, L. peploides subsp. montevidensis (Spreng.) P.H.Raven (here after Lpm), and L. grandiflora subsp. hexapetala (Hook. & Arn.) G.L.Nesom & Kartesz (here after Lgh), based on their cytotypes (2n = 16, and 2n = 80, respectively) and without evidence of hybridization between them. Furthermore, despite a predominantly vegetative reproduction observed for both species, they differed in their breeding systems. While Lpm is self-compatible and produce a high number of viable seeds in all populations, Lgh is self-incompatible and its populations may drastically differ in seed viability (Dandelot 2004). Several years later, Portillo-Lemus et al. (2021) determined that the differences in seed production between some populations of Lgh are due to the existence of a heteromorphic reproductive system in this taxon, involving a self-incompatible morph (long-style morph; hereafter L-morph), and a self-compatible morph (short-style morph: hereafter S-morph). Moreover, Portillo-Lemus et al. (2022) observed that self-pollen in the L-morph flowers stop growing lately (i.e., in the ovarian area) without fertilizing the ovules, concluding that a late-acting self-incompatible system (hereafter, LSI) is present in this morph. At this point, it is relevant to understand the possible interactions between populations of different morphs in Lgh, and the implications that they may have on their expansive success in non-native areas in order to develop more effective management plans. To achieve this goal, Stoeckel et al. (2024) analyzed the population genetics in 53 Lgh populations in western Europe (without finding any Lpm population in the sampling area), 40 of which exclusively presented the L-morph and 13 the S-morph. This fact offered the opportunity to compare and interpret the differences between populations of different morphs in Lgh. Other previous works on genetic diversity of Lgh in peripatric or non-native areas pointed to a high clonality and an extremely low genetic diversity (Okada et al. 2009, Armitage et al. 2013), concluding in a monoclonal or few ancestral original clones for these invasive populations. However, the investigations of Stoeckel et al. (2024) found a high genetic diversity in all populations of Lgh studied despite their predominant clonal reproduction. Interestingly, they found that sexual reproduction is also present, not only in the S-morph by selfing, but also in the L-morph, although limited and preferably by allogamy. They discuss the advantages and drawbacks of the different modes of reproduction observed in Lgh populations, the interactions among them, and the implications that both, the scarcely documented LSI (Gibbs 2014) and selfing, have in the reproductive success and in the maintenance of the high genetic diversity observed in Lgh in western Europe. The contrasting results with the previous ones (Okada et al. 2009, Armitage et al. 2013) stress the relevance of using appropriate markers and analyses to assess the genetic diversity in autoployploid species, as well as the necessity of knowing the modes of reproduction in the populations studied for an optimal interpretation of the genetic metrics. The approach of the study by Stoeckel et al. (2024) had the challenge of having found suitable markers to deal with a taxon of complex origin such as Lgh, whose genome is compound by a set of autotetraploid chromosomes shared with Lpm and traces of ancient hybridizations of other diploid lineages (Barloy et al. 2024). Using RAD-Seq, Stoeckel et al. (2024) generated an original set of 36 polymorphic SNPs shared between Lgh and Lpm ensuring that these SNPs belong to the tetraploid part of the Lgh genome derived from Lpm. Another interesting contribution of this work is the exhaustive analysis of several genetic descriptors (indexes) and the interpretative guide they provide for each of them in relation to the different modes of reproduction of the study system. Finally, they propose a pair of very useful synthetic indices (i.e., clonality index and selfing index), since they allow to classify populations according to their levels of clonality and selfing. Stoeckel et al. (2024) conclude the relevance that selfing and LSI populations, and the hybridization between them may have on the expansion and success of invasive plant species, and the necessity to know the modes of reproduction of these populations jointly with their genetic diversity in order to develop appropriate management plans. This study raises new questions such as the modes of reproduction and genetic diversity and structure have other Lgh populations, both invasive and native, and the dynamics of these populations under different future scenarios. References Armitage, J. D., Könyves, K., Bailey, J. P., David, J. C., & Culham, A. (2013). A molecular, morphological and cytological investigation of the identity of non-native Ludwigia (Onagraceae) populations in Britain. New Journal of Botany, 3(2), 88–95. https://doi.org/10.1179/2042349713Y.0000000023 Barloy, D., Lemus, L. P.-, Krueger-Hadfield, S. A., Huteau, V., & Coriton, O. (2024). Genomic relationships among diploid and polyploid species of the genus Ludwigia L. section Jussiaea using a combination of cytogenetic, morphological, and crossing investigations. ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.01.02.522458 Dandelot, S. (2004). Les Ludwigia spp. invasives du Sud de la France: Historique, Biosystématique, Biologie et Ecologie [PhD thesis, Aix-Marseille 3]. https://www.theses.fr/2004AIX30052 Dandelot, S., Verlaque, R., Dutartre, A., & Cazaubon, A. (2005). Ecological, dynamic and taxonomic problems due to Ludwigia (Onagraceae) in France. Hydrobiologia, 551(1), 131–136. https://doi.org/10.1007/s10750-005-4455-0 Gibbs, P. E. (2014). Late-acting self-incompatibility – the pariah breeding system in flowering plants. New Phytologist, 203(3), 717–734. https://doi.org/10.1111/nph.12874 Okada, M., Grewell, B. J., & Jasieniuk, M. (2009). Clonal spread of invasive Ludwigia hexapetala and L. grandiflora in freshwater wetlands of California. Aquatic Botany, 91(3), 123–129. https://doi.org/10.1016/j.aquabot.2009.03.006 Portillo Lemus, L. O., Bozec, M., Harang, M., Coudreuse, J., Haury, J., Stoeckel, S., & Barloy, D. (2021). Self-incompatibility limits sexual reproduction rather than environmental conditions in an invasive water primrose. Plant-Environment Interactions, 2(2), 74–86. https://doi.org/10.1002/pei3.10042 Portillo Lemus, L. O., Harang, M., Bozec, M., Haury, J., Stoeckel, S., & Barloy, D. (2022). Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heteromorphic invasive populations of Ludwigia grandiflora subsp. hexapetala. Peer Community Journal, 2. https://doi.org/10.24072/pcjournal.108 Stoeckel, S., Becheler, R., Portillo-Lemus, L., Harang, M., Besnard, A.-L., Lassalle, G., Causse-Védrines, R., Michon-Coudouel, S., Park D. J., Pope, B. J., Petit, E. J. & Barloy, D. (2024) Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western Europe. biorxiv, ver.4 peer-reviewed and recommended by PCI Evol Biol https://doi.org/10.1101/2024.03.21.586104 | Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid *Ludwigia grandiflora* subsp. hexapetala in western Europe | Solenn Stoeckel, Ronan Becheler, Luis Portillo-Lemus, Marilyne Harang, Anne-Laure Besnard, Gilles Lassalle, Romain Causse-Védrines, Sophie Michon-Coudouel, Daniel J. Park, Bernard J. Pope, Eric J. Petit, Dominique Barloy | <p>Reproductive mode, i.e., the proportion of individuals produced by clonality, selfing and outcrossing in populations, determines how hereditary material is transmitted through generations. It shapes genetic diversity and its structure over time... | ![]() | Evolutionary Applications, Evolutionary Ecology, Population Genetics / Genomics, Reproduction and Sex | Ines Alvarez | 2024-03-25 10:33:17 | View | |
03 Aug 2017
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Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradientsNoémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin, Thomas Lenormand https://doi.org/10.1111/evo.13111What doesn’t kill us makes us stronger: can Fisher’s Geometric model predict antibiotic resistance evolution?Recommended by Inês Fragata and Claudia BankThe increasing number of reported cases of antibiotic resistance is one of today’s major public health concerns. Dealing with this threat involves understanding what drives the evolution of antibiotic resistance and investigating whether we can predict (and subsequently avoid or circumvent) it [1]. References [1] Palmer AC, and Kishony R. 2013. Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nature Review Genetics 14: 243—248. doi: 10.1038/nrg3351 [2] Tenaillon O. 2014. The utility of Fisher’s geometric model in evolutionary genetics. Annual Review of Ecology, Evolution and Systematics 45: 179—201. doi: 10.1146/annurev-ecolsys-120213-091846 [3] Blanquart F and Bataillon T. 2016. Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher’s geometric model? Genetics 203: 847—862. doi: 10.1534/genetics.115.182691 [4] Harmand N, Gallet R, Jabbour-Zahab R, Martin G and Lenormand T. 2017. Fisher’s geometrical model and the mutational patterns of antibiotic resistance across dose gradients. Evolution 71: 23—37. doi: 10.1111/evo.13111 [5] de Visser, JAGM, and Krug J. 2014. Empirical fitness landscapes and the predictability of evolution. Nature 15: 480—490. doi: 10.1038/nrg3744 [6] Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S and Kishony R. 2015. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications 6: 1—8. doi: 10.1038/ncomms8385 | Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradients | Noémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin, Thomas Lenormand | <p>Fisher's geometrical model (FGM) has been widely used to depict the fitness effects of mutations. It is a general model with few underlying assumptions that gives a large and comprehensive view of adaptive processes. It is thus attractive in se... | ![]() | Adaptation | Inês Fragata | 2017-08-01 16:06:02 | View | |
03 Jun 2018
![]() Cost of resistance: an unreasonably expensive conceptThomas Lenormand, Noemie Harmand, Romain Gallet https://doi.org/10.1101/276675Let’s move beyond costs of resistance!Recommended by Inês Fragata and Claudia BankThe increase in the prevalence of (antibiotic) resistance has become a major global health concern and is an excellent example of the impact of real-time evolution on human society. This has led to a boom of studies that investigate the mechanisms and factors involved in the evolution of resistance, and to the spread of the concept of "costs of resistance". This concept refers to the relative fitness disadvantage of a drug-resistant genotype compared to a non-resistant reference genotype in the ancestral (untreated) environment. In their paper, Lenormand et al. [1] discuss the history of this concept and highlight its caveats and limitations. The authors address both practical and theoretical problems that arise from the simplistic view of "costly resistance" and argue that they can be prejudicial for antibiotic resistance studies. For a better understanding, they visualize their points of critique by means of Fisher's Geometric model. The authors give an interesting historical overview of how the concept arose and speculate that it emerged (during the 1980s) in an attempt by ecologists to spread awareness that fitness can be environment-dependent, and because of the concept's parallels to trade-offs in life-history evolution. They then identify several problems that arise from the concept, which, besides the conceptual misunderstandings that they can cause, are important to keep in mind when designing experimental studies. The authors highlight and explain the following points: Lenormand et al.'s paper [1] is a timely perspective piece in light of the ever-increasing efforts to understand and tackle resistance evolution [2]. Although some readers may shy away from the rather theoretical presentation of the different points of concern, it will be useful for both theoretical and empirical readers by illustrating the misconceptions that can arise from the concept of the cost of resistance. Ultimately, the main lesson to be learned from this paper may not be to ban the term "cost of resistance" from one's vocabulary, but rather to realize that the successful fight against drug resistance requires more differential information than the measurement of fitness effects in a drug-treated vs. non-treated environment in the lab [3-4]. Specifically, a better integration of the ecological aspects of drug resistance evolution and maintenance is needed [5], and we are far from a general understanding of how environmental factors interact and influence an organism's (absolute and relative) fitness and the effect of resistance mutations. References [1] Lenormand T, Harmand N, Gallet R. 2018. Cost of resistance: an unreasonably expensive concept. bioRxiv 276675, ver. 3 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/276675 | Cost of resistance: an unreasonably expensive concept | Thomas Lenormand, Noemie Harmand, Romain Gallet | <p>The cost of resistance, or the fitness effect of resistance mutation in absence of the drug, is a very widepsread concept in evolutionary genetics and beyond. It has represented an important addition to the simplistic view that resistance mutat... | ![]() | Adaptation, Evolutionary Applications, Evolutionary Ecology, Evolutionary Theory, Experimental Evolution, Genotype-Phenotype, Population Genetics / Genomics | Inês Fragata | 2018-03-09 02:22:07 | View | |
23 Apr 2020
![]() How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridisJulien Foucaud, Ruth A. Hufbauer, Virginie Ravigné, Laure Olazcuaga, Anne Loiseau, Aurelien Ausset, Su Wang, Lian-Sheng Zang, Nicolas Lemenager, Ashraf Tayeh, Arthur Weyna, Pauline Gneux, Elise Bonnet, Vincent Dreuilhe, Bastien Poutout, Arnaud Estoup, Benoit Facon https://doi.org/10.1101/849968Selection on a single trait does not recapitulate the evolution of life-history traits seen during an invasionRecommended by Inês Fragata and Ben Phillips based on reviews by 2 anonymous reviewersBiological invasions are natural experiments, and often show that evolution can affect dynamics in important ways [1-3]. While we often think of invasions as a conservation problem stemming from anthropogenic introductions [4,5], biological invasions are much more commonplace than this, including phenomena as diverse as natural range shifts, the spread of novel pathogens, and the growth of tumors. A major question across all these settings is which set of traits determine the ability of a population to invade new space [6,7]. Traits such as: increased growth or reproductive rate, dispersal ability and ability to defend from predation often show large evolutionary shifts across invasion history [1,6,8]. Are such multi-trait shifts driven by selection on multiple traits, or a correlated response by multiple traits to selection on one? Resolving this question is important for both theoretical and practical reasons [9,10]. But despite the importance of this issue, it is not easy to perform the necessary manipulative experiments [9]. References [1] Sakai, A.K., Allendorf, F.W., Holt, J.S. et al. (2001). The population biology of invasive species. Annual review of ecology and systematics, 32(1), 305-332. doi: 10.1146/annurev.ecolsys.32.081501.114037 | How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridis | Julien Foucaud, Ruth A. Hufbauer, Virginie Ravigné, Laure Olazcuaga, Anne Loiseau, Aurelien Ausset, Su Wang, Lian-Sheng Zang, Nicolas Lemenager, Ashraf Tayeh, Arthur Weyna, Pauline Gneux, Elise Bonnet, Vincent Dreuilhe, Bastien Poutout, Arnaud Est... | <p>Experiments comparing native to introduced populations or distinct introduced populations to each other show that phenotypic evolution is common and often involves a suit of interacting phenotypic traits. We define such sets of traits that evol... | ![]() | Adaptation, Evolutionary Applications, Experimental Evolution, Life History, Quantitative Genetics | Inês Fragata | 2019-11-29 07:07:00 | View | |
11 Oct 2021
![]() Landscape connectivity alters the evolution of density-dependent dispersal during pushed range expansionsMaxime Dahirel, Aline Bertin, Vincent Calcagno, Camille Duraj, Simon Fellous, Géraldine Groussier, Eric Lombaert, Ludovic Mailleret, Anaël Marchand, Elodie Vercken https://doi.org/10.1101/2021.03.03.433752Phenotypic evolution during range expansions is contingent on connectivity and density dependenceRecommended by Inês Fragata based on reviews by 3 anonymous reviewersUnderstanding the mechanisms underlying range expansions is key for predicting species distributions in response to environmental changes (such as global warming) and managing the global expansion of invasive species (Parmesan 2006; Suarez & Tsutsui 2008). Traditionally, two types of ecological processes were studied as essential in shaping range expansion: dispersal and population growth. However, ecology and evolution are intertwined in range expansions, as phenotypic evolution of traits involved in demographic and dispersal patterns and processes can affect and be affected by ecological dynamics, representing a full eco-evolutionary loop (Williams et al. 2019; Miller et al. 2020). Range expansions can be characterized by the type of population growth and dispersal, divided into pushed or pulled range expansions. Species that have high dispersal and high population growth at low densities present pulled range expansions (pulled by individuals from the edge populations). In contrast, populations presenting increased growth rate at intermediate densities (due to Allee effects - Allee & Bowen 1932; i.e. where growth rate decreases at lower densities) and high dispersal at high densities present pushed range expansions (driven by individuals from core and intermediate populations) (Gandhi et al. 2016). Importantly, the type of expansion is expected to have very different consequences on the genetic (and therefore) phenotypic composition of core and edge populations. Specifically, genetic variability is expected to be lower in populations experiencing pulled expansions and higher in populations involved in pushed expansions (Gandhi et al. 2016; Miller et al. 2020). However, it is not always possible to distinguish between pulled and pushed expansions, as variation in speed and shape can overlap between the two types. In addition, it is difficult to experimentally manipulate the strength of the Allee effect to create pushed versus pulled expansions. Thus, several critical predictions regarding the genetic and phenotypic composition of pulled and pushed expansions are lacking empirical tests (but see Gandhi et al. 2016). In a previous study, Dahirel et al. (2021a) combined simulations and experimental evolution of the small wasps Trichogramma brassicae to show that low connectivity led to more pushed expansions, and higher connectivity generated more pulled expansions. In accordance with theoretical predictions, this led to reduced genetic diversity in pulled expansions, and the reverse pattern in pushed expansions. However, the question of how pulled and pushed expansions affect trait evolution remained unanswered. In this follow-up study, Dahirel et al. (2021b) tackled this issue and linked the changes in connectivity and type of expansion with the phenotypic evolution of several traits using individuals from their previous experiment. Namely, the authors compared core and edge populations with founder strains to test how evolution in pushed vs. pulled expansions affected wasp size, short movement, fecundity, dispersal, and density dependent dispersal. When density dependence was not accounted for, phenotypic changes in edge populations did not match the expectations from changes in expansion dynamics. This could be due to genetic trade-offs between traits that limit phenotypic evolution (Urquhart & Williams 2021). However, when accounting for density dependent dispersal, Dahirel et al. (2021b) observed that more connected landscapes (with pulled expansions) showed positive density dispersal in core populations and negative density dispersal in edge populations, similarly to other studies (e.g. Fronhofer et al. 2017). Interestingly, in pushed (with lower connectivity) landscapes, such shift was not observed. Instead, edge populations maintained positive density dispersal even after 14 generations of expansion, whereas core populations showed higher dispersal at lower density. The authors suggest that this seemingly contradictory result is due to a combination of three processes: 1) the expansion reduced positive density dispersal in edge populations; 2) reduced connectivity directly increased dispersal costs, increasing high density dispersal; and 3) reduced connectivity indirectly caused demographic stochasticity (and reduced temporal variability in patches) leading to higher dispersal at low density in core populations. However, these results must be taken with a grain of salt, since only one of the four experimental replicates were used in the density dependent dispersal experiment. In range expansions experiments, replication is fundamental, since stochastic processes (such as gene surfing, where alleles maybe rise in frequency due by chance) are prevalent (Miller et al. 2020), and results are highly dependent on sample size, or number of replicate populations analysed. Having said that, results from Dahirel et al. (2021b) highlight the importance to contextualize the management of invasions and species distribution, since it is thought that pulled expansions are more prevalent in nature, but pushed expansions can be more important in scenarios where patchiness is high, such as urban landscapes. Moreover, Dahirel's et al. (2021b) study is a first step showing that accounting for trait density dependence is crucial when following phenotypic evolution during range expansion, and that evolution of density dependent traits may be constrained by landscape conditions. This highlights the need to account for both connectivity and density dependence to draw more accurate predictions on the evolutionary and ecological outcomes of range expansions. Allee WC, Bowen ES (1932) Studies in animal aggregations: Mass protection against colloidal silver among goldfishes. Journal of Experimental Zoology, 61, 185–207. https://doi.org/10.1002/jez.1400610202 Dahirel M, Bertin A, Calcagno V, Duraj C, Fellous S, Groussier G, Lombaert E, Mailleret L, Marchand A, Vercken E (2021a) Landscape connectivity alters the evolution of density-dependent dispersal during pushed range expansions. bioRxiv, 2021.03.03.433752, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.03.03.433752 Dahirel M, Bertin A, Haond M, Blin A, Lombaert E, Calcagno V, Fellous S, Mailleret L, Malausa T, Vercken E (2021b) Shifts from pulled to pushed range expansions caused by reduction of landscape connectivity. Oikos, 130, 708–724. https://doi.org/10.1111/oik.08278 Fronhofer EA, Gut S, Altermatt F (2017) Evolution of density-dependent movement during experimental range expansions. Journal of Evolutionary Biology, 30, 2165–2176. https://doi.org/10.1111/jeb.13182 Gandhi SR, Yurtsev EA, Korolev KS, 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, 6922–6927. https://doi.org/10.1073/pnas.1521056113 Miller TEX, Angert AL, Brown CD, Lee-Yaw JA, Lewis M, Lutscher F, Marculis NG, Melbourne BA, Shaw AK, Szűcs M, Tabares O, Usui T, Weiss-Lehman C, Williams JL (2020) Eco-evolutionary dynamics of range expansion. Ecology, 101, e03139. https://doi.org/10.1002/ecy.3139 Parmesan C (2006) Ecological and Evolutionary Responses to Recent Climate Change. Annual Review of Ecology, Evolution, and Systematics, 37, 637–669. https://doi.org/10.1146/annurev.ecolsys.37.091305.110100 Suarez AV, Tsutsui ND (2008) The evolutionary consequences of biological invasions. Molecular Ecology, 17, 351–360. https://doi.org/10.1111/j.1365-294X.2007.03456.x Urquhart CA, Williams JL (2021) Trait correlations and landscape fragmentation jointly alter expansion speed via evolution at the leading edge in simulated range expansions. Theoretical Ecology. https://doi.org/10.1007/s12080-021-00503-z Williams JL, Hufbauer RA, Miller TEX (2019) How Evolution Modifies the Variability of Range Expansion. Trends in Ecology & Evolution, 34, 903–913. https://doi.org/10.1016/j.tree.2019.05.012 | Landscape connectivity alters the evolution of density-dependent dispersal during pushed range expansions | Maxime Dahirel, Aline Bertin, Vincent Calcagno, Camille Duraj, Simon Fellous, Géraldine Groussier, Eric Lombaert, Ludovic Mailleret, Anaël Marchand, Elodie Vercken | <p style="text-align: justify;">As human influence reshapes communities worldwide, many species expand or shift their ranges as a result, with extensive consequences across levels of biological organization. Range expansions can be ranked on a con... | ![]() | Evolutionary Ecology, Experimental Evolution | Inês Fragata | 2021-03-05 17:15:46 | View |
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