Latest recommendations
Id | Title | Authors | Abstract | Picture | Thematic fields | Recommender▼ | Reviewers | Submission date | |
---|---|---|---|---|---|---|---|---|---|
25 Mar 2019
The joint evolution of lifespan and self-fertilisationThomas Lesaffre, Sylvain Billiard https://doi.org/10.1101/420877Evolution of selfing & lifespan 2.0Recommended by Thomas Bataillon based on reviews by 2 anonymous reviewersFlowering plants display a staggering diversity of both mating systems and life histories, ranging from almost exclusively selfers to obligate outcrossers, very short-lived annual herbs to super long lived trees. One pervasive pattern that has attracted considerable attention is the tight correlation that is found between mating systems and lifespan [1]. Until recently, theoretical explanations for these patterns have relied on static models exploring the consequences of several non-mutually exclusive important process: levels of inbreeding depression and ability to successfully were center stage. This make sense: successful colonization after long‐distance dispersal is far more likely to happen for self‐compatible than for self‐incompatible individuals in a sexually reproducing species. Furthermore, inbreeding depression (essentially a genetically driven phenomenon) and reproductive insurance are expected to shape the evolution of both mating system and lifespan. References | The joint evolution of lifespan and self-fertilisation | Thomas Lesaffre, Sylvain Billiard | <p>In Angiosperms, there exists a strong association between mating system and lifespan. Most self-fertilising species are short-lived and most predominant or obligate outcrossers are long-lived. This association is generally explained by the infl... | Evolutionary Theory, Life History, Reproduction and Sex | Thomas Bataillon | 2018-09-19 10:03:51 | View | ||
07 Nov 2017
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfersCédric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, and Eric Tannier 10.1101/127548Dating nodes in a phylogeny using inferred horizontal gene transfersRecommended by Tatiana Giraud and Toni Gabaldon based on reviews by Alexandros Stamatakis, Mukul Bansal and 2 anonymous reviewersDating nodes in a phylogeny is an important problem in evolution and is typically performed by using molecular clocks and fossil age estimates [1]. The manuscript by Chauve et al. [2] reports a novel method, which uses lateral gene transfers to help ordering nodes in a species tree. The idea is that a lateral gene transfer can only occur between two species living at the same time, which indirectly informs on node relative ages in a phylogeny: the donor species cannot be more recent than the recipient species. Horizontal gene transfers are increasingly recognized as frequent, even in eukaryotes, and especially in micro-organisms that have little fossil records [3-7]. Yet, such an important source of information has been very rarely used so far for inferring relative node ages in phylogenies. In this context, the method by Chauve et al. [2] represents an innovative and original approach to a difficult problem. An obvious limitation of the approach is that it relies on inferences of horizontal transfers, which detection is in itself a difficult problem. Incomplete taxon sampling, or the extinction of the true donor lineage may render patterns difficult to interpret in a temporary fashion. Yet, for clades with no fossils this may be the only piece of information we have at hand, and the growing amount of sequence data is likely to minimize issues derived from incomplete sampling. The developed method, MaxTiC (for Maximal Time Consistency) [2], represents a very nice application of theoretical developments on the well-known « Feedback Arc Set » computer science problem to the evolutionary question of ordering nodes in a phylogeny. MaxTiC uses as input a species tree and a set of time constraints based on lateral gene transfers inferred using other softwares, and minimizes conflicts between node ordering and these time constraints. The application of MaxTiC on simulated datasets indicated that node ordering was fairly accurate [2]. MaxTiC is implemented in a freely available software, which represents original and relevant contribution to the field of evolutionary biology. References [1] Donoghue P and Smith M, editors. 2003. Telling the evolutionary time. CRC press. [2] Chauve C, Rafiey A, Davin AA, Scornavacca C, Veber P, Boussau B, Szöllősi GJ, Daubin V and Tannier E. 2017. MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers. bioRxiv 127548, ver. 6 of 6th November 2017. doi: 10.1101/127548 [3] Ropars J, Rodríguez de la Vega RC, Lopez-Villavicencio M, Gouzy J, Sallet E, Debuchy R, Dupont J, Branca A and Giraud T. 2015. Adaptive horizontal gene transfers between multiple cheese-associated fungi. Current Biology 19, 2562–2569. doi: 10.1016/j.cub.2015.08.025 [4] Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras JL, Wincker P, Casaregola S and Dequin S. 2009. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proceeding of the National Academy of Science USA, 106, 16333–16338. doi: 10.1073/pnas.0904673106 [5] Naranjo-Ortíz MA, Brock M, Brunke S, Hube B, Marcet-Houben M, Gabaldón T. 2016. Widespread inter- and intra-domain horizontal gene transfer of d-amino acid metabolism enzymes in Eukaryotes. Frontiers in Microbiology 7, 2001. doi: 10.3389/fmicb.2016.02001 [6] Alexander WG, Wisecaver JH, Rokas A, Hittinger CT. 2016. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proceeding of the National Academy of Science USA. 113, 4116–4121. doi: 10.1073/pnas.1517242113 [7] Marcet-Houben M, Gabaldón T. 2010. Acquisition of prokaryotic genes by fungal genomes. Trends in Genetics. 26, 5–8. doi: 10.1016/j.tig.2009.11.007 | MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers | Cédric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, and Eric Tannier | Lateral gene transfers (LGTs) between ancient species contain information about the relative timing of species diversification. Specifically, the ancestors of a donor species must have existed before the descendants of the recipient species. Hence... | Bioinformatics & Computational Biology, Evolutionary Dynamics, Genome Evolution, Life History, Molecular Evolution, Phylogenetics / Phylogenomics | Tatiana Giraud | 2017-06-28 13:40:52 | View | ||
19 Feb 2018
Genomic imprinting mediates dosage compensation in a young plant XY systemAline Muyle, Niklaus Zemp, Cecile Fruchard, Radim Cegan, Jan Vrana, Clothilde Deschamps, Raquel Tavares, Franck Picard, Roman Hobza, Alex Widmer, Gabriel Marais https://doi.org/10.1101/179044Dosage compensation by upregulation of maternal X alleles in both males and females in young plant sex chromosomesRecommended by Tatiana Giraud and Judith Mank based on reviews by 3 anonymous reviewersSex chromosomes evolve as recombination is suppressed between the X and Y chromosomes. The loss of recombination on the sex-limited chromosome (the Y in mammals) leads to degeneration of both gene expression and gene content for many genes [1]. Loss of gene expression or content from the Y chromosome leads to differences in gene dose between males and females for X-linked genes. Because expression levels are often correlated with gene dose [2], these hemizygous genes have a lower expression levels in the heterogametic sex. This in turn disrupts the stoichiometric balance among genes in protein complexes that have components on both the sex chromosomes and autosomes [3], which could have serious deleterious consequences for the heterogametic sex. References | Genomic imprinting mediates dosage compensation in a young plant XY system | Aline Muyle, Niklaus Zemp, Cecile Fruchard, Radim Cegan, Jan Vrana, Clothilde Deschamps, Raquel Tavares, Franck Picard, Roman Hobza, Alex Widmer, Gabriel Marais | <p>During the evolution of sex chromosomes, the Y degenerates and its expression gets reduced relative to the X and autosomes. Various dosage compensation mechanisms that recover ancestral expression levels in males have been described in animals.... | Bioinformatics & Computational Biology, Expression Studies, Genome Evolution, Molecular Evolution, Reproduction and Sex | Tatiana Giraud | 2017-09-20 20:39:46 | View | ||
21 Nov 2022
Artisanal and farmers bread making practices differently shape fungal species community composition in French sourdoughsElisa Michel, Estelle Masson, Sandrine Bubbendorf, Leocadie Lapicque, Thibault Nidelet, Diego Segond, Stephane Guezenec, Therese Marlin, Hugo deVillers, Olivier Rue, Bernard Onno, Judith Legrand, Delphine Sicard https://doi.org/10.1101/679472The variety of bread-making practices promotes diversity conservation in food microbial communitiesRecommended by Tatiana Giraud and Jeanne Ropars based on reviews by 2 anonymous reviewersDomesticated organisms are excellent models for understanding ecology and evolution and they are important for our food production and safety. While less studied than plants and animals, micro-organisms have also been domesticated, in particular for food fermentation [1]. The most studied domesticated micro-organism is the yeast used to make wine, beer and bread, Saccharomyces cerevisiae [2, 3, 4]. Filamentous fungi used for cheese-making have recently gained interest, for example Penicillium roqueforti used to make blue cheeses and P. camemberti to make soft cheeses [5, 6, 7, 8]. As for plants and animals, domestication has led to beneficial traits for food production in fermenting fungi, but also to bottlenecks and degeneration [6, 7, 9]; P. camemberti for example does not produce enough spores any more for optimal culture and inoculation and P. roqueforti has lost sexual fertility [9]. The loss of genetic diversity and of species diversity in our food production system is concerning for multiple reasons : i) it jeopardizes future improvement in the face of global changes ; ii) it causes the loss of evolved diversity during centuries under human selection, and therefore of beneficial characteristics and specificities that we may never be able to recover ; iii) it leads to degeneration in the few cultivated strains; iv) it impoverishes the diversity of our food products and local adaptation of production practices. The study of domesticated fungi used for food fermentation has focused so far on the evolution of lineages and on their metabolic specificities. Microbiological assemblages and species diversity have been much less studied, while they likely also have a strong impact on the quality and safety of final products. This study by Elisa Michel and colleagues [10] addresses this question, using an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyse bread-making practices and their impact on microbial communities in sourdough. Elisa Michel and colleagues [10] identified two distinct groups of bread-making practices based on interviews and surveys, with farmer-like practices (low bread production, use of ancient wheat populations, manual kneading, working at ambient temperature, long fermentation periods and no use of commercial baker’s yeast) versus more intensive, artisanal-like practices. Metabarcoding and microbial culture-based analyses showed that the well-known baker’s yeast, Saccharomyces cerevisiae, was, surprisingly, not the most common species in French organic sourdoughs. Kazachstania was the most represented yeast genus over all sourdoughs, both in terms of read abundance and of species diversity. Kazachstania species were also often dominant in individual sourdoughs, but Saccharomyces uvarum or Torulaspora delbrueckii could also be the dominant yeast species. Metabarcoding analyses further revealed that the composition of the fungal communities differed between the farmer-like and more intensive practices, representing the first evidence of the influence of artisanal practices on microbial communities. The fungal communities were impacted by a combination of bread-making variables including the type of wheat varieties, the length of fermentation, the quantity of bread made per week and the use of commercial yeast. Maintaining on farm less intensive bread-making practices, may allow the preservation of typical species and phenotypic diversity in microbial communities in sourdough. Farmer-like practices did not lead to higher diversity within sourdoughs but, overall, the diversity of bread-making practices allow maintaining a larger diversity in sourdoughs. For example, different Kazachstania species were most abundant in sourdoughs from artisanal-like and farmer-like practices. Interviews with the bakers suggested the role of dispersal of Kazachstania species in shaping sourdough microbial communities, dispersal occurring by seed exchanges, sourdough mixing or gifts, bread-making training in common or working in one another’s bakery. Nikolai Vavilov [11] had already highlighted for crops the importance of isolated cultures and selection in different farms for generating and preserving crop diversity, but also the importance of seed exchange for fostering adaptation. Furthermore, one of the yeast frequently found in artisanal sourdoughs, Kazachstania humilis, displayed phenotypic differences between sourdough and non-sourdough strains, suggesting domestication. The sourdough strains exhibited significantly higher CO2 production rate and a lower fermentation latency-phase time. The study by Elisa Michel and colleagues [10] is thus novel and inspiring in showing the importance of interdisciplinary studies, combining metabarcoding, microbiology and interviews for assessing the composition and diversity of microbial communities in human-made food, and in revealing the impact of artisanal-like bread-making practices in preserving microbial community diversity. Interdisciplinary studies are still rare but have already shown the importance of combining ethno-ecology, biology and evolution to decipher the role of human practices on genetic diversity in crops, animals and food microorganisms and to help preserving genetic resources [12]. For example, in the case of the bread wheat Triticum aestivum, such interdisciplinary studies have shown that genetic diversity has been shaped by farmers’ seed diffusion and farming practices [13]. We need more of such interdisciplinary studies on the impact of farmer versus industrial agricultural and food-making practices as we urgently need to preserve the diversity of micro-organisms used in food production that we are losing at a rapid pace [6, 7, 14]. References [1] Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse M-A (2017) Fungi as a Source of Food. Microbiology Spectrum, 5, 5.3.09. https://doi.org/10.1128/microbiolspec.FUNK-0030-2016 [2] Legras J-L, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, Marcet-Houben M, Gabaldon T, Schuller D, Sampaio JP, Dequin S (2018) Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. Molecular Biology and Evolution, 35, 1712–1727. https://doi.org/10.1093/molbev/msy066 [3] Bai F-Y, Han D-Y, Duan S-F, Wang Q-M (2022) The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae. Genes, 13, 230. https://doi.org/10.3390/genes13020230 [4] Fay JC, Benavides JA (2005) Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae. PLOS Genetics, 1, e5. https://doi.org/10.1371/journal.pgen.0010005 [5] Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T (2015) Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Current Biology, 25, 2562–2569. https://doi.org/10.1016/j.cub.2015.08.025 [6] Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T (2020) Independent domestication events in the blue-cheese fungus Penicillium roqueforti. Molecular Ecology, 29, 2639–2660. https://doi.org/10.1111/mec.15359 [7] Ropars J, Didiot E, Rodríguez de la Vega RC, Bennetot B, Coton M, Poirier E, Coton E, Snirc A, Le Prieur S, Giraud T (2020) Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties. Current Biology, 30, 4441-4453.e4. https://doi.org/10.1016/j.cub.2020.08.082 [8] Caron T, Piver ML, Péron A-C, Lieben P, Lavigne R, Brunel S, Roueyre D, Place M, Bonnarme P, Giraud T, Branca A, Landaud S, Chassard C (2021) Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. International Journal of Food Microbiology, 354, 109174. https://doi.org/10.1016/j.ijfoodmicro.2021.109174 [9] Ropars J, Lo Y-C, Dumas E, Snirc A, Begerow D, Rollnik T, Lacoste S, Dupont J, Giraud T, López-Villavicencio M (2016) Fertility depression among cheese-making Penicillium roqueforti strains suggests degeneration during domestication. Evolution, 70, 2099–2109. https://doi.org/10.1111/evo.13015 [10] Michel E, Masson E, Bubbendorf S, Lapicque L, Nidelet T, Segond D, Guézenec S, Marlin T, Devillers H, Rué O, Onno B, Legrand J, Sicard D, Bakers TP (2022) Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs. bioRxiv, 679472, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/679472 [11] Vavilov NI, Vavylov MI, Dorofeev VF (1992) Origin and Geography of Cultivated Plants. Cambridge University Press. [12] Saslis-Lagoudakis CH, Clarke AC (2013) Ethnobiology: the missing link in ecology and evolution. Trends in Ecology & Evolution, 28, 67–68. https://doi.org/10.1016/j.tree.2012.10.017 [13] Thomas M, Demeulenaere E, Dawson JC, Khan AR, Galic N, Jouanne-Pin S, Remoue C, Bonneuil C, Goldringer I (2012) On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat. Evolutionary Applications, 5, 779–795. https://doi.org/10.1111/j.1752-4571.2012.00257.x [14] Demeulenaere É, Lagrola M (2021) Des indicateurs pour accompagner “ les éleveurs de microbes” : Une communauté épistémique face au problème des laits “ paucimicrobiens ” dans la production fromagère au lait cru (1995-2015). Revue d’anthropologie des connaissances, 15. http://journals.openedition.org/rac/24953 | Artisanal and farmers bread making practices differently shape fungal species community composition in French sourdoughs | Elisa Michel, Estelle Masson, Sandrine Bubbendorf, Leocadie Lapicque, Thibault Nidelet, Diego Segond, Stephane Guezenec, Therese Marlin, Hugo deVillers, Olivier Rue, Bernard Onno, Judith Legrand, Delphine Sicard | <p style="text-align: justify;">Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbia... | Adaptation, Evolutionary Applications, Evolutionary Ecology | Tatiana Giraud | 2022-01-27 14:53:08 | View | ||
14 Dec 2023
Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individualsCastel J, Pradillon F, Cueff V, Leger G, Daguin-Thiébaut C, Ruault S, Mary J, Hourdez S, Jollivet D, and Broquet T https://doi.org/10.1101/2023.04.11.536409A shared XY sex chromosome system with variable recombination ratesRecommended by Tanja Schwander based on reviews by Hugo Darras, Daniel Jeffries and 1 anonymous reviewerMany species with separate sexes have evolved sex chromosomes, with the sex-limited chromosomes (i.e. the Y or W chromosomes) exhibiting a wide range of genetic divergences from their homologous X or Z chromosomes (Bachtrog et al., 2014). Variable divergences can result from the cessation of recombination between sex chromosomes that occurred at different time points, with the mechanisms of initiation and expansion of recombination suppression along sex chromosomes remaining poorly understood (Charlesworth, 2017). The study by Castel et al (2023) describes the serendipitous discovery of a shared XY sex chromosome system in three closely related hydrothermal vent gastropods. The X and Y chromosomes appear to still recombine but at variable rates across the three species. This variation makes the gastropod system a very promising focus for future research on sex chromosome evolution. An additional intriguing finding is that some females in one of three gastropod species contain male reproductive tissue in their gonads, providing a fascinating case of a mixed or transitory sexual system. Overall, the study by Castel et al (2023) offers the first insights into the reproduction and sex chromosome system of animals living in deep marine vents, which have remained poorly studied and open outstanding research perspectives on these creatures. References Bachtrog, D., J.E.Mank, C.L.Peichel, M.Kirkpatrick, S.P.Otto, T.L. Ashman, M.W.Hahn, J.Kitano, I.Mayrose, R.Ming, et al. 2014.Sex determination: why so many ways of doing it? PLoSBiol. 12:e1001899. https://doi.org/10.1371/journal.pbio.1001899 Charlesworth, D. Young sex chromosomes in plants and animals. 2019. New Phytologist 224: 1095–1107. https://doi.org/10.1111/nph.16002 Castel J, Pradillon F, Cueff V, Leger G, Daguin-Thiébaut C, Ruault S, Mary J, Hourdez S, Jollivet D, and Broquet T 2023. Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.04.11.536409 | Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals | Castel J, Pradillon F, Cueff V, Leger G, Daguin-Thiébaut C, Ruault S, Mary J, Hourdez S, Jollivet D, and Broquet T | <p style="text-align: justify;">Molluscs have a wide variety of sexual systems and have undergone many transitions from separate sexes to hermaphroditism or vice versa, which is of interest for studying the evolution of sex determination and diffe... | Population Genetics / Genomics, Reproduction and Sex | Tanja Schwander | 2023-04-14 11:48:25 | View | ||
03 Jun 2019
Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory networkMaud Irène Tenaillon, Khawla Sedikki, Maeva Mollion, Martine Le Guilloux, Elodie Marchadier, Adrienne Ressayre, Christine Dillmann https://doi.org/10.1101/461947Early and late flowering gene expression patterns in maizeRecommended by Tanja Pyhäjärvi based on reviews by Laura Shannon and 2 anonymous reviewersArtificial selection experiments are key experiments in evolutionary biology. The demonstration that application of selective pressure across multiple generations results in heritable phenotypic changes is a tangible and reproducible proof of the evolution by natural selection. References [1] Hill, W. G., & Caballero, A. (1992). Artificial selection experiments. Annual Review of Ecology and Systematics, 23(1), 287-310. doi: 10.1146/annurev.es.23.110192.001443 | Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network | Maud Irène Tenaillon, Khawla Sedikki, Maeva Mollion, Martine Le Guilloux, Elodie Marchadier, Adrienne Ressayre, Christine Dillmann | <p>Artificial selection experiments are designed to investigate phenotypic evolution of complex traits and its genetic basis. Here we focused on flowering time, a trait of key importance for plant adaptation and life-cycle shifts. We undertook div... | Adaptation, Experimental Evolution, Expression Studies, Quantitative Genetics | Tanja Pyhäjärvi | 2018-11-23 11:57:35 | View | ||
20 Jan 2020
A young age of subspecific divergence in the desert locust Schistocerca gregaria, inferred by ABC Random ForestMarie-Pierre Chapuis, Louis Raynal, Christophe Plantamp, Christine N. Meynard, Laurence Blondin, Jean-Michel Marin, Arnaud Estoup https://doi.org/10.1101/671867Estimating recent divergence history: making the most of microsatellite data and Approximate Bayesian Computation approachesRecommended by Takeshi Kawakami and Concetta Burgarella based on reviews by Michael D Greenfield and 2 anonymous reviewersThe present-day distribution of extant species is the result of the interplay between their past population demography (e.g., expansion, contraction, isolation, and migration) and adaptation to the environment. Shedding light on the timing and magnitude of key demographic events helps identify potential drivers of such events and interaction of those drivers, such as life history traits and past episodes of environmental shifts. The understanding of the key factors driving species evolution gives important insights into how the species may respond to changing conditions, which can be particularly relevant for the management of harmful species, such as agricultural pests (e.g. [1]). Meaningful demographic inferences present major challenges. These include formulating evolutionary scenarios fitting species biology and the eco-geographical context and choosing informative molecular markers and accurate quantitative approaches to statistically compare multiple demographic scenarios and estimate the parameters of interest. A further issue comes with result interpretation. Accurately dating the inferred events is far from straightforward since reliable calibration points are necessary to translate the molecular estimates of the evolutionary time into absolute time units (i.e. years). This can be attempted in different ways, such as by using fossil and archaeological records, heterochronous samples (e.g. ancient DNA), and/or mutation rate estimated from independent data (e.g. [2], [3] for review). Nonetheless, most experimental systems rarely meet these conditions, hindering the comprehensive interpretation of results. The contribution of Chapuis et al. [4] addresses these issues to investigate the recent history of the African insect pest Schistocerca gregaria (desert locust). They apply Approximate Bayesian Computation-Random Forest (ABC-RF) approaches to microsatellite markers. Owing to their fast mutation rate microsatellite markers offer at least two advantages: i) suitability for analyzing recently diverged populations, and ii) direct estimate of the germline mutation rate in pedigree samples. The work of Chapuis et al. [4] benefits of both these advantages, since they have estimates of mutation rate and allele size constraints derived from germline mutations in the species [5]. The main aim of the study is to infer the history of divergence of the two subspecies of the desert locust, which have spatially disjoint distribution corresponding to the dry regions of North and West-South Africa. They first use paleo-vegetation maps to formulate hypotheses about changes in species range since the last glacial maximum. Based on them, they generate 12 divergence models. For the selection of the demographic model and parameter estimation, they apply the recently developed ABC-RF approach, a powerful inferential tool that allows optimizing the use of summary statistics information content, among other advantages [6]. Some methodological novelties are also introduced in this work, such as the computation of the error associated with the posterior parameter estimates under the best scenario. The accuracy of timing estimate is assured in two ways: i) by the use of microsatellite markers with known evolutionary dynamics, as underlined above, and ii) by assessing the divergence time threshold above which posterior estimates are likely to be biased by size homoplasy and limits in allele size range [7]. The best-supported model suggests a recent divergence event of the subspecies of S. gregaria (around 2.6 kya) and a reduction of populations size in one of the subspecies (S. g. flaviventris) that colonized the southern distribution area. As such, results did not support the hypothesis that the southward colonization was driven by the expansion of African dry environments associated with the last glacial maximum, as it has been postulated for other arid-adapted species with similar African disjoint distributions [8]. The estimated time of divergence points at a much more recent origin for the two subspecies, during the late Holocene, in a period corresponding to fairly stable arid conditions similar to current ones [9,10]. Although the authors cannot exclude that their microsatellite data bear limited information on older colonization events than the last one, they bring arguments in favour of alternative explanations. The hypothesis privileged does not involve climatic drivers, but the particularly efficient dispersal behaviour of the species, whose individuals are able to fly over long distances (up to thousands of kilometers) under favourable windy conditions. A single long-distance dispersal event by a few individuals would explain the genetic signature of the bottleneck. There is a growing number of studies in phylogeography in arid regions in the Southern hemisphere, but the impact of past climate changes on the species distribution in this region remains understudied relative to the Northern hemisphere [11,12]. The study presented by Chapuis et al. [4] offers several important insights into demographic changes and the evolutionary history of an agriculturally important pest species in Africa, which could also mirror the history of other organisms in the continent. As the authors point out, there are necessarily some uncertainties associated with the models of past ecosystems and climate, especially for Africa. Interestingly, the authors argue that the information on paleo-vegetation turnover was more informative than climatic niche modeling for the purpose of their study since it made them consider a wider range of bio-geographical changes and in turn a wider range of evolutionary scenarios (see discussion in Supplementary Material). Microsatellite markers have been offering a useful tool in population genetics and phylogeography for decades, but their popularity is perhaps being taken over by single nucleotide polymorphism (SNP) genotyping and whole-genome sequencing (WGS) (the peak year of the number of the publication with “microsatellite” is in 2012 according to PubMed). This study reaffirms the usefulness of these classic molecular markers to estimate past demographic events, especially when species- and locus-specific microsatellite mutation features are available and a powerful inferential approach is adopted. Nonetheless, there are still hurdles to overcome, such as the limitations in scenario choice associated with the simulation software used (e.g. not allowing for continuous gene flow in this particular case), which calls for further improvement of simulation tools allowing for more flexible modeling of demographic events and mutation patterns. In sum, this work not only contributes to our understanding of the makeup of the African biodiversity but also offers a useful statistical framework, which can be applied to a wide array of species and molecular markers (microsatellites, SNPs, and WGS). References [1] Lehmann, P. et al. (2018). Complex responses of global insect pests to climate change. bioRxiv, 425488. doi: https://dx.doi.org/10.1101/425488 [2] Donoghue, P. C., & Benton, M. J. (2007). Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends in Ecology & Evolution, 22(8), 424-431. doi: https://dx.doi.org/10.1016/j.tree.2007.05.005 [3] Ho, S. Y., Lanfear, R., Bromham, L., Phillips, M. J., Soubrier, J., Rodrigo, A. G., & Cooper, A. (2011). Time‐dependent rates of molecular evolution. Molecular ecology, 20(15), 3087-3101. doi: https://dx.doi.org/10.1111/j.1365-294X.2011.05178.x [4] Chapuis, M.-P., Raynal, L., Plantamp, C., Meynard, C. N., Blondin, L., Marin, J.-M. and Estoup, A. (2020). A young age of subspecific divergence in the desert locust Schistocerca gregaria, inferred by ABC Random Forest. bioRxiv, 671867, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. doi: https://dx.doi.org/10.1101/671867 5] Chapuis, M.-P., Plantamp, C., Streiff, R., Blondin, L., & Piou, C. (2015). Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations. Molecular ecology, 24(24), 6107-6119. doi: https://dx.doi.org/10.1111/mec.13465 [6] Raynal, L., Marin, J. M., Pudlo, P., Ribatet, M., Robert, C. P., & Estoup, A. (2018). ABC random forests for Bayesian parameter inference. Bioinformatics, 35(10), 1720-1728. doi: https://dx.doi.org/10.1093/bioinformatics/bty867 [7] Estoup, A., Jarne, P., & Cornuet, J. M. (2002). Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular ecology, 11(9), 1591-1604. doi: https://dx.doi.org/10.1046/j.1365-294X.2002.01576.x [8] Moodley, Y. et al. (2018). Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum). Proceedings of the Royal Society B, 285(1890), 20181567. doi: https://dx.doi.org/10.1098/rspb.2018.1567 [9] Kröpelin, S. et al. (2008). Climate-driven ecosystem succession in the Sahara: the past 6000 years. science, 320(5877), 765-768. doi: https://dx.doi.org/10.1126/science.1154913 [10] Maley, J. et al. (2018). Late Holocene forest contraction and fragmentation in central Africa. Quaternary Research, 89(1), 43-59. doi: https://dx.doi.org/10.1017/qua.2017.97 [11] Beheregaray, L. B. (2008). Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17(17), 3754-3774. doi: https://dx.doi.org/10.1111/j.1365-294X.2008.03857.x [12] Dubey, S., & Shine, R. (2012). Are reptile and amphibian species younger in the Northern Hemisphere than in the Southern Hemisphere?. Journal of evolutionary biology, 25(1), 220-226. doi: https://dx.doi.org/10.1111/j.1420-9101.2011.02417.x ***** A video about this preprint is available here: | A young age of subspecific divergence in the desert locust Schistocerca gregaria, inferred by ABC Random Forest | Marie-Pierre Chapuis, Louis Raynal, Christophe Plantamp, Christine N. Meynard, Laurence Blondin, Jean-Michel Marin, Arnaud Estoup | <p>Dating population divergence within species from molecular data and relating such dating to climatic and biogeographic changes is not trivial. Yet it can help formulating evolutionary hypotheses regarding local adaptation and future responses t... | Bioinformatics & Computational Biology, Evolutionary Applications, Phylogeography & Biogeography, Population Genetics / Genomics | Takeshi Kawakami | 2019-06-20 10:31:15 | View | ||
16 Dec 2022
Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depressionDiala Abu Awad, Donald Waller https://doi.org/10.1101/2021.12.16.473022Pseudo-overdominance: how linkage and selection can interact and oppose to purging of deleterious mutations.Recommended by Sylvain Glémin based on reviews by Yaniv Brandvain, Lei Zhao and 1 anonymous reviewerMost mutations affecting fitness are deleterious and they have many evolutionary consequences. The dynamics and consequences of deleterious mutations are a long-standing question in evolutionary biology and a strong theoretical background has already been developed, for example, to predict the mutation load, inbreeding depression or background selection. One of the classical results is that inbreeding helps purge partially recessive deleterious mutations by exposing them to selection in homozygotes. However, this mainly results from single-locus considerations. When interactions among several, more or less linked, deleterious mutations are taken into account, peculiar dynamics can emerge. One of them, called pseudo-overdominance (POD), corresponds to the maintenance in a population of two (or more) haplotype blocks composed of several recessive deleterious mutations in repulsion that mimics overdominance. Indeed, homozygote individuals for one of the haplotype blocks expose many deleterious mutations to selection whereas they are reciprocally masked in heterozygotes, leading to higher fitness of heterozygotes compared to both homozygotes. A related process, called associative overdominance (AOD) is the effect of such deleterious alleles in repulsion on the linked neutral variation that can be increased by AOD. Although this possibility has been recognized for a long time (Otha and Kimura 1969), it has been mainly considered an anecdotal process. Recently, both theoretical (Zhao and Charlesworth 2016) and genomic analyses (Gilbert et al. 2020) have renewed interest in such a process, suggesting that it could be important in weakly recombining regions of a genome. Donald Waller (2021) - one of the co-authors of the current work - also recently proposed that POD could be quantitatively important with broad implications, and could resolve some unexplained observations such as the maintenance of inbreeding depression in highly selfing species. Yet, a proper theoretical framework analysing the effect of inbreeding on POD was lacking. In this theoretical work, Diala Abu Awad and Donald Waller (2022) addressed this question through an elegant combination of analytical predictions and intensive multilocus simulations. They determined the conditions under which POD can be maintained and how long it could resist erosion by recombination, which removes the negative association between deleterious alleles (repulsion) at the core of the mechanism. They showed that under tight linkage, POD regions can persist for a long time and generate substantial segregating load and inbreeding depression, even under inbreeding, so opposing (for a while) to the purging effect. They also showed that background selection can affect the genomic structure of POD regions by rapidly erasing weak POD regions but maintaining strong POD regions (i.e with many tightly linked deleterious alleles). These results have several implications. They can explain the maintenance of inbreeding depression despite inbreeding (as anticipated by Waller 2021), which has implications for the evolution of mating systems. If POD can hardly emerge under high selfing, it can persist from an outcrossing ancestor long after the transition towards a higher selfing rate and could explain the maintenance of mixed mating systems(which is possible with true overdominance, see Uyenoyama and Waller 1991). The results also have implications for genomic analyses, pointing to regions of low or no recombination where POD could be maintained, generating both higher diversity and heterozygosity than expected and variance in fitness. As structural variations are likely widespread in genomes with possible effects on suppressing recombination (Mérot et al. 2020), POD regions should be checked more carefully in genomic analyses (see also Gilbert et al. 2020). Overall, this work should stimulate new theoretical and empirical studies, especially to assess how quantitatively strong and widespread POD can be. It also stresses the importance of properly considering genetic linkage genome-wide, and so the role of recombination landscapes in determining patterns of diversity and fitness effects. References
Awad DA, Waller D (2022) Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression. bioRxiv, 2021.12.16.473022, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.12.16.473022 Gilbert KJ, Pouyet F, Excoffier L, Peischl S (2020) Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination. Current Biology, 30, 101-107.e3. https://doi.org/10.1016/j.cub.2019.11.063 Mérot C, Oomen RA, Tigano A, Wellenreuther M (2020) A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation. Trends in Ecology & Evolution, 35, 561–572. https://doi.org/10.1016/j.tree.2020.03.002 Ohta T, Kimura M (1969) Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics, 63, 229–238. https://doi.org/10.1093/genetics/63.1.229 Uyenoyama MK, Waller DM (1991) Coevolution of self-fertilization and inbreeding depression II. Symmetric overdominance in viability. Theoretical Population Biology, 40, 47–77. https://doi.org/10.1016/0040-5809(91)90046-I Waller DM (2021) Addressing Darwin’s dilemma: Can pseudo-overdominance explain persistent inbreeding depression and load? Evolution, 75, 779–793. https://doi.org/10.1111/evo.14189 Zhao L, Charlesworth B (2016) Resolving the Conflict Between Associative Overdominance and Background Selection. Genetics, 203, 1315–1334. https://doi.org/10.1534/genetics.116.188912 | Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression | Diala Abu Awad, Donald Waller | <p style="text-align: justify;">Classical models that ignore linkage predict that deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. True overdomina... | Evolutionary Dynamics, Evolutionary Theory, Genome Evolution, Hybridization / Introgression, Population Genetics / Genomics, Reproduction and Sex | Sylvain Glémin | 2022-01-04 12:15:35 | View | ||
31 Mar 2017
POSTPRINT
Human adaptation of Ebola virus during the West African outbreakUrbanowicz, R.A., McClure, C.P., Sakuntabhai, A., Sall, A.A., Kobinger, G., Müller, M.A., Holmes, E.C., Rey, F.A., Simon-Loriere, E., and Ball, J.K. 10.1016/j.cell.2016.10.013Ebola evolution during the 2013-2016 outbreakRecommended by Sylvain Gandon and Sébastien LionThe Ebola virus (EBOV) epidemic that started in December 2013 resulted in around 28,000 cases and more than 11,000 deaths. Since the emergence of the disease in Zaire in 1976 the virus had produced a number of outbreaks in Africa but until 2013 the reported numbers of human cases had never risen above 500. Could this exceptional epidemic size be due to the spread of a human-adapted form of the virus? The large mutation rate of the virus [1-2] may indeed introduce massive amounts of genetic variation upon which selection may act. Several earlier studies based on the accumulation of genome sequences sampled during the epidemic led to contrasting conclusions. A few studies discussed evidence of positive selection on the glycoprotein that may be linked to phenotypic variations on infectivity and/or immune evasion [3-4]. But the heterogeneity in the transmission of some lineages could also be due to environmental heterogeneity and/or stochasticity. Most studies could not rule out the null hypothesis of the absence of positive selection and human adaptation [1-2 and 5]. In a recent experimental study, Urbanowicz et al. [6] chose a different method to tackle this question. A phylogenetic analysis of genome sequences from viruses sampled in West Africa revealed the existence of two main lineages (one with a narrow geographic distribution in Guinea, and the other with a wider geographic distribution) distinguished by a single amino acid substitution in the glycoprotein of the virus (A82V), and of several sub-lineages characterised by additional substitutions. The authors used this phylogenetic data to generate a panel of mutant pseudoviruses and to test their ability to infect human and fruit bat cells. These experiments revealed that specific amino acid substitutions led to higher infectivity of human cells, including A82V. This increased infectivity on human cells was associated with a decreased infectivity in fruit bat cell cultures. Since fruit bats are likely to be the reservoir of the virus, this paper indicates that human adaptation may have led to a specialization of the virus to a new host. An accompanying paper in the same issue of Cell by Diehl et al. [7] reports results that confirm the trend identified by Urbanowicz et al. [6] and further indicate that the increased infectivity of A82V is specific for primate cells. Diehl et al. [7] also report some evidence for higher virulence of A82V in humans. In other words, the evolution of the virus may have led to higher abilities to infect and to kill its novel host. This work thus confirms the adaptive potential of RNA virus and the ability of Ebola to specialize to a novel host. In this context, the availability of an effective vaccine against the disease is particularly welcome [8]. The study of Urbanowicz et al. [6] is also remarkable because it illustrates the need of experimental approaches for the study of phenotypic variation when inference methods based on phylodynamics fail to extract a clear biological message. The analysis of genomic evolution is still in its infancy and there is a need for new theoretical developments to help detect more rapidly candidate mutations involved in adaptations to new environmental conditions. References [1] Gire, S.K., Goba, A., Andersen, K.G., Sealfon, R.S.G., Park, D.J., Kanneh, L., Jalloh, S., Momoh, M., Fullah, M., Dudas, G., et al. (2014). Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369–1372. doi: 10.1126/science.1259657 | Human adaptation of Ebola virus during the West African outbreak | Urbanowicz, R.A., McClure, C.P., Sakuntabhai, A., Sall, A.A., Kobinger, G., Müller, M.A., Holmes, E.C., Rey, F.A., Simon-Loriere, E., and Ball, J.K. | The 2013–2016 outbreak of Ebola virus (EBOV) in West Africa was the largest recorded. It began following the cross-species transmission of EBOV from an animal reservoir, most likely bats, into humans, with phylogenetic analysis revealing the co-ci... | Adaptation, Evolutionary Epidemiology, Genome Evolution, Genotype-Phenotype, Molecular Evolution, Species interactions | Sylvain Gandon | 2017-03-31 14:20:38 | View | ||
17 Feb 2020
Epistasis, inbreeding depression and the evolution of self-fertilizationDiala Abu Awad and Denis Roze https://doi.org/10.1101/809814Epistasis and the evolution of selfingRecommended by Sylvain Gandon based on reviews by Nick Barton and 1 anonymous reviewerThe evolution of selfing results from a balance between multiple evolutionary forces. Selfing provides an "automatic advantage" due to the higher efficiency of selfers to transmit their genes via selfed and outcrossed offspring. Selfed offspring, however, may suffer from inbreeding depression. In principle the ultimate evolutionary outcome is easy to predict from the relative magnitude of these two evolutionary forces [1,2]. Yet, several studies explicitly taking into account the genetic architecture of inbreeding depression noted that these predictions are often too restrictive because selfing can evolve in a broader range of conditions [3,4]. References [1] Holsinger, K. E., Feldman, M. W., and Christiansen, F. B. (1984). The evolution of self-fertilization in plants: a population genetic model. The American Naturalist, 124(3), 446-453. doi: 10.1086/284287 | Epistasis, inbreeding depression and the evolution of self-fertilization | Diala Abu Awad and Denis Roze | <p>Inbreeding depression resulting from partially recessive deleterious alleles is thought to be the main genetic factor preventing self-fertilizing mutants from spreading in outcrossing hermaphroditic populations. However, deleterious alleles may... | Evolutionary Theory, Quantitative Genetics, Reproduction and Sex | Sylvain Gandon | 2019-10-18 09:29:41 | View |
MANAGING BOARD
Guillaume Achaz
Juan Arroyo
Trine Bilde
Dustin Brisson
Marianne Elias
Inês Fragata
Matteo Fumagalli
Tatiana Giraud
Frédéric Guillaume
Ruth Hufbauer
Sara Magalhaes
Caroline Nieberding
Michael David Pirie
Tanja Pyhäjärvi
Tanja Schwander
Alejandro Gonzalez Voyer