|Id||Title||Authors||Abstract||Picture||Thematic fields||Recommender▲||Reviewers||Submission date|
20 Nov 2017
Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selectionDiala Abu Awad and Denis Roze 10.1101/180000
Understanding genetic variance, load, and inbreeding depression with selfingRecommended by Aneil F. Agrawal based on reviews by Frédéric Guillaume and 1 anonymous reviewer
A classic problem in evolutionary biology is to understand the genetic variance in fitness. The simplest hypothesis is that variation exists, even in well-adapted populations, as a result of the balance between mutational input and selective elimination. This variation causes a reduction in mean fitness, known as the mutation load. Though mutation load is difficult to quantify empirically, indirect evidence of segregating genetic variation in fitness is often readily obtained by comparing the fitness of inbred and outbred offspring, i.e., by measuring inbreeding depression. Mutation-selection balance models have been studied as a means of understanding the genetic variance in fitness, mutation load, and inbreeding depression. Since their inception, such models have increased in sophistication, allowing us to ask these questions under more realistic and varied scenarios. The new theoretical work by Abu Awad and Roze  is a substantial step forward in understanding how arbitrary levels of self-fertilization affect variation, load and inbreeding depression under mutation-selection balance.
 Abu Awad D and Roze D. 2017. Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection. bioRxiv, 180000, ver. 4 of 17th November 2017. doi: 10.1101/180000
 Lande R. 1977. The influence of the mating system on the maintenance of genetic variability in polygenic characters. Genetics 86: 485–498.
 Charlesworth D and Charlesworth B. 1987. Inbreeding depression and its evolutionary consequences. Annual Review of Ecology and Systematics. 18: 237–268. doi: 10.1111/10.1146/annurev.es.18.110187.001321
 Lande R and Porcher E. 2015. Maintenance of quantitative genetic variance under partial self-fertilization, with implications for the evolution of selfing. Genetics 200: 891–906. doi: 10.1534/genetics.115.176693
 Roze D. 2015. Effects of interference between selected loci on the mutation load, inbreeding depression, and heterosis. Genetics 201: 745–757. doi: 10.1534/genetics.115.178533
 Martin G and Lenormand T. 2006. A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species. Evolution 60: 893–907. doi: 10.1111/j.0014-3820.2006.tb01169.x
 Martin G, Elena SF and Lenormand T. 2007. Distributions of epistasis in microbes fit predictions from a fitness landscape model. Nature Genetics 39: 555–560. doi: 10.1038/ng1998
|Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection||Diala Abu Awad and Denis Roze||The mating system of a species is expected to have important effects on its genetic diversity. In this paper, we explore the effects of partial selfing on the equilibrium genetic variance Vg, mutation load L and inbreeding depression δ under stabi...||Evolutionary Theory, Population Genetics / Genomics, Quantitative Genetics, Reproduction and Sex||Aneil F. Agrawal||2017-08-26 09:29:20||View|
14 Mar 2017
Evolution of multiple sensory systems drives novel egg-laying behavior in the fruit pest Drosophila suzukiiMarianthi Karageorgi, Lasse B. Bräcker, Sébastien Lebreton, Caroline Minervino, Matthieu Cavey, K.P. Siju, Ilona C. Grunwald Kadow, Nicolas Gompel, Benjamin Prud’homme https://doi.org/10.1016/j.cub.2017.01.055
A valuable work lying at the crossroad of neuro-ethology, evolution and ecology in the fruit pest Drosophila suzukiiRecommended by Arnaud Estoup and Ruth Arabelle Hufbauer
Adaptations to a new ecological niche allow species to access new resources and circumvent competitors and are hence obvious pathways of evolutionary success. The evolution of agricultural pest species represents an important case to study how a species adapts, on various timescales, to a novel ecological niche. Among the numerous insects that are agricultural pests, the ability to lay eggs (or oviposit) in ripe fruit appears to be a recurrent scenario. Fruit flies (family Tephritidae) employ this strategy, and include amongst their members some of the most destructive pests (e.g., the olive fruit fly Bactrocera olea or the medfly Ceratitis capitata). In their ms, Karageorgi et al.  studied how Drosophila suzukii, a new major agricultural pest species that recently invaded Europe and North America, evolved the novel behavior of laying eggs into undamaged fresh fruit. The close relatives of D. suzukii lay their eggs on decaying plant substrates, and thus this represents a marked change in host use that links to substantial economic losses to the fruit industry. Although a handful of studies have identified genetic changes causing new behaviors in various species, the question of the evolution of behavior remains a largely uncharted territory. The study by Karageorgi et al.  represents an original and most welcome contribution in this domain for a non-model species. Using clever behavioral experiments to compare D. suzukii to several related Drosophila species, and complementing those results with neurogenetics and mutant analyses using D. suzukii, the authors nicely dissect the sensory changes at the origin of the new egg-laying behavior. The experiments they describe are easy to follow, richly illustrate through figures and images, and particularly well designed to progressively decipher the sensory bases driving oviposition of D. suzukii on ripe fruit. Altogether, Karageorgi et al.’s  results show that the egg-laying substrate preference of D. suzukii has considerably evolved in concert with its morphology (especially its enlarged, serrated ovipositor that enables females to pierce the skin of many ripe fruits). Their observations clearly support the view that the evolution of traits that make D. suzukii an agricultural pest included the modification of several sensory systems (i.e. mechanosensation, gustation and olfaction). These differences between D. suzukii and its close relatives collectively underlie a radical change in oviposition behavior, and were presumably instrumental in the expansion of the ecological niche of the species. The authors tentatively propose a multi-step evolutionary scenario from their results with the emergence of D. suzukii as a pest species as final outcome. Such formalization represents an interesting evolutionary model-framework that obviously would rely upon further data and experiments to confirm and refine some of the evolutionary steps proposed, especially the final and recent transition of D. suzukii from non-invasive to invasive species.
 Karageorgi M, Bräcker LB, Lebreton S, Minervino C, Cavey M, Siju KP, Grunwald Kadow IC, Gompel N, Prud’homme B. 2017. Evolution of multiple sensory systems drives novel egg-laying behavior in the fruit pest Drosophila suzukii. Current Biology, 27: 1-7. doi: 10.1016/j.cub.2017.01.055
|Evolution of multiple sensory systems drives novel egg-laying behavior in the fruit pest Drosophila suzukii||Marianthi Karageorgi, Lasse B. Bräcker, Sébastien Lebreton, Caroline Minervino, Matthieu Cavey, K.P. Siju, Ilona C. Grunwald Kadow, Nicolas Gompel, Benjamin Prud’homme||The rise of a pest species represents a unique opportunity to address how species evolve new behaviors and adapt to novel ecological niches. We address this question by studying the egg-laying behavior of Drosophila suzukii, an invasive agricultur...||Adaptation, Behavior & Social Evolution, Evo-Devo, Evolutionary Applications, Evolutionary Ecology, Expression Studies, Genotype-Phenotype, Macroevolution, Molecular Evolution||Arnaud Estoup||2017-03-13 17:42:00||View|
03 Oct 2018
Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plantsAndrew J. Tanentzap, Javier Igea, Matthew G. Johnston, Matthew J. Larcombe https://doi.org/10.1101/152215
Are both very young and the very old plant lineages at heightened risk of extinction?Recommended by Arne Mooers based on reviews by Dan Greenberg and 1 anonymous reviewer
Human economic activity is responsible for the vast majority of ongoing extinction, but that does not mean lineages are being affected willy-nilly. For amphibians  and South African flowering plants , young species have a somewhat higher than expected chance of being threatened with extinction. In contrast, older Australian marsupial lineages seem to be more at risk . Both of the former studies suggested that situations leading to peripheral isolation might simultaneously increase ongoing speciation and current threat via small geographic range, while the authors of the latter study suggested that older species might have evolved increasingly narrow niches. Here, Andrew Tanentzap and colleagues  dig deeper into the putative links between species age, niche breadth and threat status. Across 500-some plant genera worldwide, they find that, indeed, ""younger"" species (i.e. from younger and faster-diversifying genera) were more likely to be listed as imperiled by the IUCN, consistent with patterns for amphibians and African plants. Given this, results from their finer-level analyses of conifers are initially bemusing: here, ""older"" (i.e., on longer terminal branches) species were at higher risk. This would make conifers more like Australian marsupials, with the rest of the plants being more like amphibians. However, here where the data were more finely grained, the authors detected a second interesting pattern: using an intriguing matched-pair design, they detect a signal of conifer species niches seemingly shrinking as a function of age. The authors interpret this as consistent with increasing specialization, or loss of ancestral warm wet habitat, over paleontological time. It is true that conifers in general are older than plants more generally, with some species on branches that extend back many 10s of millions of years, and so a general loss of suitable habitat makes some sense. If so, both the pattern for all plants (small initial ranges heightening extinction) and the pattern for conifers (eventual increasing specialization or habitat contraction heightening extinction) could occur, each on a different time scale. As a coda, the authors detected no effect of age on threat status in palms; however, this may be both because palms have already lost species to climate-change induced extinction, and because they are thought to speciate more via long-distance dispersal and adaptive divergence then via peripheral isolation.
 Greenberg, D. A., & Mooers, A. Ø. (2017). Linking speciation to extinction: Diversification raises contemporary extinction risk in amphibians. Evolution Letters, 1, 40–48. doi: 10.1002/evl3.4
|Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plants||Andrew J. Tanentzap, Javier Igea, Matthew G. Johnston, Matthew J. Larcombe||<p>Extinction threatens many species, yet few factors predict this risk across the plant Tree of Life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and adaptive zones varies with time, but evidence fo...||Macroevolution, Phylogenetics / Phylogenomics, Phylogeography & Biogeography||Arne Mooers||2018-02-01 21:01:19||View|
14 Dec 2016
High Rates of Species Accumulation in Animals with Bioluminescent Courtship DisplaysEllis EA, Oakley TH 10.1016/j.cub.2016.05.043
Bioluminescent sexually selected traits as an engine for biodiversity across animal speciesRecommended by Astrid Groot and Carole Smadja
In evolutionary biology, sexual selection is hypothesized to increase speciation rates in animals, as theory predicts that sexual selection will contribute to phenotypic diversification and affect rates of species accumulation at macro-evolutionary time scales. However, testing this hypothesis and gathering convincing evidence have proven difficult. Although some studies have shown a strong correlation between proxies of sexual selection and species diversity (mostly in birds), this relationship relies on some assumptions on the link between these proxies and the strength of sexual selection and is not detected in some other taxa, making taxonomically widespread conclusions impossible.
In a recent study published in Current Biology , Ellis and Oakley provide strong evidence that bioluminescent sexual displays have driven high species richness in taxonomically diverse animal lineages, providing a crucial link between sexual selection and speciation.
Ellis and Oakley  explored the scientific literature for well-resolved evolutionary trees with branches containing bioluminescent lineages and identified lineages that use light for courtship or camouflage in a wide range of marine and terrestrial taxa including insects, crustaceans, cephalopods, segmented worms, and fishes. The researchers counted the number of species in each bioluminescent clade and found that all groups with light-courtship displays had more species and faster rates of species accumulation than their non-luminous most closely related sister lineages or ancestors. In contrast, those groups that used bioluminescence for predator avoidance had a lower than expected rate of species richness on average.
Nicely encompassing a diversity of taxa and neatly controlling for the rate of species accumulation of the encompassing clade, the results of Ellis and Oakley are clear-cut and provide the most comprehensive evidence to date for the hypothesis that sexual displays can act as drivers of speciation. One question this study incites is what is happening in terms of sexual selection in species displaying defensive bioluminescence or no bioluminescence at all: do those lineages use no mating signals at all or other mating signals that are less apparent, and will those experience lower levels of sexual selection than bioluminescent mating signals, i.e. consistent with Ellis and Oakley results? It would also be interesting to investigate the diversification rates in animal species using other modalities, such as chemical, acoustic or any other type of signals used by males, females or both sexes, to determine what types of sexual signals may be more generally drivers of speciation.
 Ellis EA, Oakley TH. 2016. High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays. Current Biology 26:1916–1921. doi: 10.1016/j.cub.2016.05.043
 Davis MP, Holcroft NI, Wiley EO, Sparks JS, Smith WL. 2014. Species-specific bioluminescence facilitates speciation in the deep sea. Marine Biology 161:11391148. doi: 10.1007/s00227-014-2406-x
 Davis MP, Sparks JS, Smith WL. 2016. Repeated and Widespread Evolution of Bioluminescence in Marine Fishes. PLoS One 11:e0155154. doi: 10.1371/journal.pone.0155154
 Claes JM, Nilsson D-E, Mallefet J, Straube N. 2015. The presence of lateral photophores correlates with increased speciation in deep-sea bioluminescent sharks. Royal Society Open Science 2:150219. doi: 10.1098/rsos.150219
|High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays||Ellis EA, Oakley TH||One of the great mysteries of evolutionary biology is why closely related lineages accumulate species at different rates. Theory predicts that populations undergoing strong sexual selection will more quickly differentiate because of increased pote...||Adaptation, Evolutionary Ecology, Sexual Selection, Speciation||Astrid Groot||2016-12-14 19:01:59||View|
25 Jun 2020
Transcriptional differences between the two host strains of Spodoptera frugiperda (Lepidoptera: Noctuidae)Marion Orsucci, Yves Moné, Philippe Audiot, Sylvie Gimenez, Sandra Nhim, Rima Naït-Saïdi, Marie Frayssinet, Guillaume Dumont, Jean-Paul Boudon, Marin Vabre, Stéphanie Rialle, Rachid Koual, Gael J. Kergoat, Rodney N. Nagoshi, Robert L. Meagher, Emmanuelle d'Alencon, Nicolas Nègre https://doi.org/10.1101/263186
Speciation through selection on mitochondrial genes?Recommended by Astrid Groot based on reviews by Heiko Vogel and Sabine Haenniger
Whether speciation through ecological specialization occurs has been a thriving research area ever since Mayr (1942) stated this to play a central role. In herbivorous insects, ecological specialization is most likely to happen through host plant differentiation (Funk et al. 2002). Therefore, after Dorothy Pashley had identified two host strains in the Fall armyworm (FAW), Spodoptera frugiperda, in 1988 (Pashley 1988), researchers have been trying to decipher the evolutionary history of these strains, as this seems to be a model species in which speciation is currently occurring through host plant specialization. Even though FAW is a generalist, feeding on many different host plant species (Pogue 2002) and a devastating pest in many crops, Pashley identified a so-called corn strain and a so-called rice strain in Puerto Rico. Genetically, these strains were found to differ mostly in an esterase, although later studies showed additional genetic differences and markers, mostly in the mitochondrial COI and the nuclear TPI. Recent genomic studies showed that the two strains are overall so genetically different (2% of their genome being different) that these two strains could better be called different species (Kergoat et al. 2012). So far, the most consistent differences between the strains have been their timing of mating activities at night (Schoefl et al. 2009, 2011; Haenniger et al. 2019) and hybrid incompatibilities (Dumas et al. 2015; Kost et al. 2016). Whether and to what extent host plant preference or performance contributed to the differentiation of these sympatrically occurring strains has remained unclear.
 Dumas, P. et al. (2015). Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?. Genetica, 143(3), 305-316. doi: 10.1007/s10709-015-9829-2
|Transcriptional differences between the two host strains of Spodoptera frugiperda (Lepidoptera: Noctuidae)||Marion Orsucci, Yves Moné, Philippe Audiot, Sylvie Gimenez, Sandra Nhim, Rima Naït-Saïdi, Marie Frayssinet, Guillaume Dumont, Jean-Paul Boudon, Marin Vabre, Stéphanie Rialle, Rachid Koual, Gael J. Kergoat, Rodney N. Nagoshi, Robert L. Meagher, Emm...||<p>Spodoptera frugiperda, the fall armyworm (FAW), is an important agricultural pest in the Americas and an emerging pest in sub-Saharan Africa, India, East-Asia and Australia, causing damage to major crops such as corn, sorghum and soybean. While...||Adaptation, Evolutionary Ecology, Expression Studies, Life History, Speciation||Astrid Groot||2018-05-09 13:04:34||View|
13 Sep 2019
Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the U.S.A.Thierry De Meeûs, Cynthia T. Chan, John M. Ludwig, Jean I. Tsao, Jaymin Patel, Jigar Bhagatwala, and Lorenza Beati https://doi.org/10.1101/622373
New curation method for microsatellite markers improves population genetics analysesRecommended by Aurelien Tellier based on reviews by Eric Petit, Martin Husemann and 2 anonymous reviewers
Genetic markers are used for in modern population genetics/genomics to uncover the past neutral and selective history of population and species. Besides Single Nucleotide Polymorphisms (SNPs) obtained from whole genome data, microsatellites (or Short Tandem Repeats, SSR) have been common markers of choice in numerous population genetics studies of non-model species with large sample sizes . Microsatellites can be used to uncover and draw inference of the past population demography (e.g. expansion, decline, bottlenecks…), population split, population structure and gene flow, but also life history traits and modes of reproduction (e.g. [2,3]). These markers are widely used in conservation genetics  or to study parasites or disease vectors . Microsatellites do show higher mutation rate than SNPs increasing, on the one hand, the statistical power to infer recent events (for example crop domestication, [2,3]), while, on the other hand, decreasing their statistical power over longer time scales due to homoplasy .
 Jarne, P., and Lagoda, P. J. (1996). Microsatellites, from molecules to populations and back. Trends in ecology & evolution, 11(10), 424-429. doi: 10.1016/0169-5347(96)10049-5
|Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the U.S.A.||Thierry De Meeûs, Cynthia T. Chan, John M. Ludwig, Jean I. Tsao, Jaymin Patel, Jigar Bhagatwala, and Lorenza Beati||<p>Null alleles, short allele dominance (SAD), and stuttering increase the perceived relative inbreeding of individuals and subpopulations as measured by Wright’s FIS and FST. Ascertainment bias, due to such amplifying problems are usually caused ...||Evolutionary Ecology, Other, Population Genetics / Genomics||Aurelien Tellier||2019-05-02 20:52:08||View|
29 Nov 2022
Joint inference of adaptive and demographic history from temporal population genomic dataVitor A. C. Pavinato, Stéphane De Mita, Jean-Michel Marin, Miguel de Navascués https://doi.org/10.1101/2021.03.12.435133
Inference of genome-wide processes using temporal population genomic dataRecommended by Aurelien Tellier based on reviews by Lawrence Uricchio and 2 anonymous reviewers
Evolutionary genomics, and population genetics in particular, aim to decipher the respective influence of neutral and selective forces shaping genetic polymorphism in a species/population. This is a much-needed requirement before scanning genome data for footprints of species adaptation to their biotic and abiotic environment (Johri et al. 2022). In general, we would like to quantify the proportion of the genome evolving neutrally and under selective (positive, balancing and negative) pressures (Kern and Hahn 2018, Johri et al. 2021). We thus need to understand patterns of linked selection along the genome, that is how the distribution of genetic polymorphisms is shaped by selected sites and the recombination landscape. The present contribution by Pavinato et al. (2022) provides an additional method in the population genomics toolbox to quantify the extent of linked positive and negative selection using temporal data.
The availability of genomics data for model and non-model species has led to improvement of the modeling framework for demography and selection (Johri et al. 2022), but also new inference methods making use of the full genome data based on the Sequential Markovian Coalescent (SMC, Li and Durbin 2011), Approximate Bayesian Computation (ABC, Jay et al. 2019), ABC and machine learning (Pudlo et al. 2016, Raynal et al. 2019) or Deep Learning (Sanchez et al. 2021). These methods are based on one sample in time and the use of the coalescent theory to reconstruct the past (demographic) history. However, it is also possible to obtain for many species temporal data sampled over several time points. For species with short generation time (in experimental evolution or monitored populations), one can sample a population every couple of generations as exemplified with Drosophila melanogaster (Bergland et al. 2010). For species with longer generation times that cannot be easily regularly sampled in time, it becomes possible to sequence available specimens from museums (e.g. Cridland et al. 2018) or ancient DNA samples. Methods using temporal data are based on the classical population genomics assumption that demography (migration, population subdivision, population size changes) leaves a genome-wide signal, while selection leaves a localized signal in the close vicinity of the causal mutation. Several methods do assess the demography of a population (change in effective population size, Ne, in time) using temporal data (e.g. Jorde and Ryman 2007) which can be used to calibrate the detection of loci under strong positive selection (Foll et al. 2014). Recently Buffalo and Coop (2020) used genome-wide covariance between allele frequency changes across time samples (and across replicates) to quantify the effects of linked selection over short timescales.
In the present contribution, Pavinato et al. (2022) make use of temporal data to draw the joint estimation of demographic and selective parameters using a simulation-based method (ABC-Random Forests). This study by Pavinato et al. (2022) builds a framework allowing to infer the census size of the population in time (N) separately from the effect of genetic drift, which is determined by change in effective population size (Ne) in time, as well estimates of genome-wide parameters of selection. In a nutshell, the authors use a forward simulator and summarize genome data by genomic windows using classic statistics (nucleotide diversity, Tajima’s D, FST, heterozygosity) between time samples and for each sample. They specifically use the distributions (higher moments) of these statistics among all windows. The authors combine as input for the ABC-RF, vectors of summary statistics, model parameters and five latent variables: Ne, the ratio Ne/N, the number of beneficial mutations under strong selection, the average selection coeﬀicient of strongly selected mutations, and the average substitution load. Indeed, the authors are interested in three different types of selection components: 1) the adaptive potential of a population which is estimated as the population mutation rate of beneficial mutations (θb), 2) the number of mutations under strong selection (irrespective of whether they reached fixation or not), and 3) the overall population fitness which is a function of the genetic load. In other words, the novelty of this method is not to focus on the detection of loci under selection, but to infer key parameters/distributions summarizing the genome-wide signal of demography and (positive and negative) selection. As a proof of principle, the authors then apply their method to a dataset of feral populations of honey bees (Apis mellifera) collected in California across many years and recovered from Museum samples (Cridland et al. 2018). The approach yields estimates of Ne which are on the same order of magnitude of previous estimates in hymenopterans, and the authors discuss why the different populations show various values of Ne and N which can be explained by different history of admixture with wild but also domesticated lineages of bees.
This study focuses on quantifying the genome-wide joint footprints of demography, and strong positive and negative selection to determine which proportion of the genome evolves neutrally or not. Further application of this method can be anticipated, for example, to study species with ecological and life-history traits which generate discrepancies between census size and Ne, for example for plants with selfing or seed banking (Sellinger et al. 2020), and for which the genome-wide effect of linked selection is not fully understood.
Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean G, Payseur BA, Pfeifer SP, Stephan W, Jensen JD (2022) Recommendations for improving statistical inference in population genomics. PLOS Biology, 20, e3001669. https://doi.org/10.1371/journal.pbio.3001669
Kern AD, Hahn MW (2018) The Neutral Theory in Light of Natural Selection. Molecular Biology and Evolution, 35, 1366–1371. https://doi.org/10.1093/molbev/msy092
Johri P, Riall K, Becher H, Excoffier L, Charlesworth B, Jensen JD (2021) The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects. Molecular Biology and Evolution, 38, 2986–3003. https://doi.org/10.1093/molbev/msab050
Pavinato VAC, Mita SD, Marin J-M, Navascués M de (2022) Joint inference of adaptive and demographic history from temporal population genomic data. bioRxiv, 2021.03.12.435133, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.03.12.435133
Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature, 475, 493–496. https://doi.org/10.1038/nature10231
Jay F, Boitard S, Austerlitz F (2019) An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions. Molecular Biology and Evolution, 36, 1565–1579. https://doi.org/10.1093/molbev/msz038
Pudlo P, Marin J-M, Estoup A, Cornuet J-M, Gautier M, Robert CP (2016) Reliable ABC model choice via random forests. Bioinformatics, 32, 859–866. https://doi.org/10.1093/bioinformatics/btv684
Raynal L, Marin J-M, Pudlo P, Ribatet M, Robert CP, Estoup A (2019) ABC random forests for Bayesian parameter inference. Bioinformatics, 35, 1720–1728. https://doi.org/10.1093/bioinformatics/bty867
Sanchez T, Cury J, Charpiat G, Jay F (2021) Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation. Molecular Ecology Resources, 21, 2645–2660. https://doi.org/10.1111/1755-0998.13224
Bergland AO, Behrman EL, O’Brien KR, Schmidt PS, Petrov DA (2014) Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila. PLOS Genetics, 10, e1004775. https://doi.org/10.1371/journal.pgen.1004775
Cridland JM, Ramirez SR, Dean CA, Sciligo A, Tsutsui ND (2018) Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California. Genome Biology and Evolution, 10, 458–472. https://doi.org/10.1093/gbe/evy007
Jorde PE, Ryman N (2007) Unbiased Estimator for Genetic Drift and Effective Population Size. Genetics, 177, 927–935. https://doi.org/10.1534/genetics.107.075481
Foll M, Shim H, Jensen JD (2015) WFABC: a Wright–Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data. Molecular Ecology Resources, 15, 87–98. https://doi.org/10.1111/1755-0998.12280
Buffalo V, Coop G (2020) Estimating the genome-wide contribution of selection to temporal allele frequency change. Proceedings of the National Academy of Sciences, 117, 20672–20680. https://doi.org/10.1073/pnas.1919039117
Sellinger TPP, Awad DA, Moest M, Tellier A (2020) Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data. PLOS Genetics, 16, e1008698. https://doi.org/10.1371/journal.pgen.1008698
|Joint inference of adaptive and demographic history from temporal population genomic data||Vitor A. C. Pavinato, Stéphane De Mita, Jean-Michel Marin, Miguel de Navascués||<p style="text-align: justify;">Disentangling the effects of selection and drift is a long-standing problem in population genetics. Simulations show that pervasive selection may bias the inference of demography. Ideally, models for the inference o...||Adaptation, Population Genetics / Genomics||Aurelien Tellier||2021-10-20 09:41:26||View|
18 Jan 2023
The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfingEmilie Tezenas, Tatiana Giraud, Amandine Veber, Sylvain Billiard https://doi.org/10.1101/2022.10.07.511119
Maintenance of deleterious mutations and recombination suppression near mating-type loci under selfingRecommended by Aurelien Tellier based on reviews by 3 anonymous reviewers
The causes and consequences of the evolution of sexual reproduction are a major topic in evolutionary biology. With advances in sequencing technology, it becomes possible to compare sexual chromosomes across species and infer the neutral and selective processes shaping polymorphism at these chromosomes. Most sex and mating-type chromosomes exhibit an absence of recombination in large genomic regions around the animal, plant or fungal sex-determining genes. This suppression of recombination likely occurred in several time steps generating stepwise increasing genomic regions starting around the sex-determining genes. This mechanism generates so-called evolutionary strata of differentiation between sex chromosomes (Nicolas et al., 2004, Bergero and Charlesworth, 2009, Hartmann et al. 2021). The evolution of extended regions of recombination suppression is also documented on mating-type chromosomes in fungi (Hartmann et al., 2021) and around supergenes (Yan et al., 2020, Jay et al., 2021). The exact reason and evolutionary mechanisms for this phenomenon are still, however, debated.
Two hypotheses are proposed: 1) sexual antagonism (Charlesworth et al., 2005), which, nevertheless, does explain the observed occurrence of the evolutionary strata, and 2) the sheltering of deleterious alleles by inversions carrying a lower load than average in the population (Charlesworth and Wall, 1999, Antonovics and Abrams, 2004). In the latter, the mechanism is as follows. A genetic inversion or a suppressor of recombination in cis may exhibit some overdominance behaviour. The inversion exhibiting less recessive deleterious mutations (compared to others at the same locus) may increase in frequency, before at higher frequency occurring at the homozygous state, expressing its genetic load. However, the inversion may never be at the homozygous state if it is genetically linked to a gene in a permanently heterozygous state. The inversion can then be advantageous and may reach fixation at the sex chromosome (Charlesworth and Wall, 1999, Antonovics and Abrams, 2004, Jay et al., 2022). These selective mechanisms promote thus the suppression of recombination around the sex-determining gene, and recessive deleterious mutations are permanently sheltered. This hypothesis is corroborated by the sheltering of deleterious mutations observed around loci under balancing selection (Llaurens et al. 2009, Lenz et al. 2016) and around mating-type genes in fungi and supergenes (Jay et al. 2021, Jay et al., 2022).
In this present theoretical study, Tezenas et al. (2022) analyse how linkage to a necessarily heterozygous fungal mating type locus influences the persistence/extinction time of a new mutation at a second selected locus. This mutation can either be deleterious and recessive, or overdominant. There is arbitrary linkage between the two loci, and sexual reproduction occurs either between 1) gametes of different individuals (outcrossing), or 2) by selfing with gametes originating from the same (intra-tetrad) or different (inter-tetrad) tetrads produced by that individual. Note, here, that the mating-type gene does not prevent selfing. The authors study the initial stochastic dynamics of the mutation using a multi-type branching process (and simulations when analytical results cannot be obtained) to compute the extinction time of the deleterious mutation. The main result is that the presence of a mating-type locus always decreases the purging probability and increases the purging time of the mutations under selfing. Ultimately, deleterious mutations can indeed accumulate near the mating-type locus over evolutionary time scales. In a nutshell, high selfing or high intra-tetrad mating do increase the sheltering effect of the mating-type locus. In effect, the outcome of sheltering of deleterious mutations depends on two opposing mechanisms: 1) a higher selfing rate induces a greater production of homozygotes and an increased effect of the purging of deleterious mutations, while 2) a higher intra-tetrad selfing rate (or linkage with the mating-type locus) generates heterozygotes which have a small genetic load (and are favoured). The authors also show that rare events of extremely long maintenance of deleterious mutations can occur.
The authors conclude by highlighting the manifold effect of selfing which reduces the effective population size and thus impairs the efficiency of selection and increases the mutational load, while also favouring the purge of deleterious homozygous mutations. Furthermore, this study emphasizes the importance of studying the maintenance and accumulation of deleterious mutations in the vicinity of heterozygous loci (e.g. under balancing selection) in selfing species.
Antonovics J, Abrams JY (2004) Intratetrad Mating and the Evolution of Linkage Relationships. Evolution, 58, 702–709. https://doi.org/10.1111/j.0014-3820.2004.tb00403.x
Bergero R, Charlesworth D (2009) The evolution of restricted recombination in sex chromosomes. Trends in Ecology & Evolution, 24, 94–102. https://doi.org/10.1016/j.tree.2008.09.010
Charlesworth D, Morgan MT, Charlesworth B (1990) Inbreeding Depression, Genetic Load, and the Evolution of Outcrossing Rates in a Multilocus System with No Linkage. Evolution, 44, 1469–1489. https://doi.org/10.1111/j.1558-5646.1990.tb03839.x
Charlesworth D, Charlesworth B, Marais G (2005) Steps in the evolution of heteromorphic sex chromosomes. Heredity, 95, 118–128. https://doi.org/10.1038/sj.hdy.6800697
Charlesworth B, Wall JD (1999) Inbreeding, heterozygote advantage and the evolution of neo–X and neo–Y sex chromosomes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 266, 51–56. https://doi.org/10.1098/rspb.1999.0603
Hartmann FE, Duhamel M, Carpentier F, Hood ME, Foulongne-Oriol M, Silar P, Malagnac F, Grognet P, Giraud T (2021) Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes. New Phytologist, 229, 2470–2491. https://doi.org/10.1111/nph.17039
Jay P, Chouteau M, Whibley A, Bastide H, Parrinello H, Llaurens V, Joron M (2021) Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms. Nature Genetics, 53, 288–293. https://doi.org/10.1038/s41588-020-00771-1
Jay P, Tezenas E, Véber A, Giraud T (2022) Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes. PLOS Biology, 20, e3001698. https://doi.org/10.1371/journal.pbio.3001698
Lenz TL, Spirin V, Jordan DM, Sunyaev SR (2016) Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection. Molecular Biology and Evolution, 33, 2555–2564. https://doi.org/10.1093/molbev/msw127
Llaurens V, Gonthier L, Billiard S (2009) The Sheltered Genetic Load Linked to the S Locus in Plants: New Insights From Theoretical and Empirical Approaches in Sporophytic Self-Incompatibility. Genetics, 183, 1105–1118. https://doi.org/10.1534/genetics.109.102707
Nicolas M, Marais G, Hykelova V, Janousek B, Laporte V, Vyskot B, Mouchiroud D, Negrutiu I, Charlesworth D, Monéger F (2004) A Gradual Process of Recombination Restriction in the Evolutionary History of the Sex Chromosomes in Dioecious Plants. PLOS Biology, 3, e4. https://doi.org/10.1371/journal.pbio.0030004
Tezenas E, Giraud T, Véber A, Billiard S (2022) The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing. bioRxiv, 2022.10.07.511119, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.10.07.511119
Yan Z, Martin SH, Gotzek D, Arsenault SV, Duchen P, Helleu Q, Riba-Grognuz O, Hunt BG, Salamin N, Shoemaker D, Ross KG, Keller L (2020) Evolution of a supergene that regulates a trans-species social polymorphism. Nature Ecology & Evolution, 4, 240–249. https://doi.org/10.1038/s41559-019-1081-1
|The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing||Emilie Tezenas, Tatiana Giraud, Amandine Veber, Sylvain Billiard||<p style="text-align: justify;">Large regions of suppressed recombination having extended over time occur in many organisms around genes involved in mating compatibility (sex-determining or mating-type genes). The sheltering of deleterious alleles...||Evolutionary Dynamics, Evolutionary Ecology, Evolutionary Theory, Genome Evolution, Population Genetics / Genomics, Reproduction and Sex||Aurelien Tellier||2022-10-10 13:50:30||View|
13 Nov 2017
Epidemiological trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen populationFrederic Suffert, Henriette Goyeau, Ivan Sache, Florence Carpentier, Sandrine Gelisse, David Morais, Ghislain Delestre 10.1101/151068
The pace of pathogens’ adaptation to their host plantsRecommended by Benoit Moury based on reviews by Benoit Moury and 1 anonymous reviewer
Because of their shorter generation times and larger census population sizes, pathogens are usually ahead in the evolutionary race with their hosts. The risks linked to pathogen adaptation are still exacerbated in agronomy, where plant and animal populations are not freely evolving but depend on breeders and growers, and are usually highly genetically homogeneous. As a consequence, the speed of pathogen adaptation is crucial for agriculture sustainability. Unraveling the time scale required for pathogens’ adaptation to their hosts would notably greatly improve our estimation of the risks of pathogen emergence, the efficiency of disease control strategies and the design of epidemiological surveillance schemes. However, the temporal scale of pathogen evolution has received much less attention than its spatial scale . In their study of a wheat fungal disease, Suffert et al.  reached contrasting conclusions about the pathogen adaptation depending on the time scale (intra- or inter-annual) and on the host genotype (sympatric or allopatric) considered, questioning the experimental assessment of this important problem.
Suffert et al.  sampled two pairs of Zymoseptoria tritici (the causal agent of septoria leaf blotch) sub-populations in a bread wheat field plot, representing (i) isolates collected at the beginning or at the end of an epidemic in a single growing season (2009-2010 intra-annual sampling scale) and (ii) isolates collected from plant debris at the end of growing seasons in 2009 and in 2015 (inter-annual sampling scale). Then, they measured in controlled conditions two aggressiveness traits of the isolates of these four Z. tritici sub-populations, the latent period and the lesion size on leaves, on two wheat cultivars. One of the cultivars was considered as "sympatric" because it was at the source of the studied isolates and was predominant in the growing area before the experiment, whereas the other cultivar was considered as "allopatric" since it replaced the previous one and became predominant in the growing area during the sampling period.
On the sympatric host, at the intra-annual scale, they observed a marginally-significant decrease in latent period and a significant decrease of the between-isolate variance for this trait, which are consistent with a selection of pathogen variants with an enhanced aggressiveness. In contrast, at the inter-annual scale, no difference in the mean or variance of aggressiveness trait values was observed on the sympatric host, suggesting a lack of pathogen adaptation. They interpreted the contrast between observations at the two time scales as the consequence of a trade-off for the pathogen between a gain of aggressiveness after several generations of asexual reproduction at the intra-annual scale and a decrease of the probability to reproduce sexually and to be transmitted from one growing season to the next. Indeed, at the end of the growing season, the most aggressive isolates are located on the upper leaves of plants, where the pathogen density and hence probably also the probability to reproduce sexually, is lower. On the allopatric host, the conclusion about the pathogen stability at the inter-annual scale was somewhat different, since a significant increase in the mean lesion size was observed (isolates corresponding to the intra-annual scale were not checked on the allopatric host). This shows the possibility for the pathogen to evolve at the inter-annual scale, for a given aggressiveness trait and on a given host.
In conclusion, Suffert et al.’s  study emphasizes the importance of the experimental design in terms of sampling time scale and host genotype choice to analyze the pathogen adaptation to its host plants. It provides also an interesting scenario, at the crossroad of the pathogen’s reproduction regime, niche partitioning and epidemiological processes, to interpret these contrasted results. Pathogen adaptation to plant cultivars with major-effect resistance genes is usually fast, including in the wheat-Z. tritici system . Therefore, this study will be of great help for future studies on pathogen adaptation to plant partial resistance genes and on strategies of deployment of such resistance at the landscape scale.
 Suffert F, Goyeau H, Sache I, Carpentier F, Gelisse S, Morais D and Delestre G. 2017. Epidemiological trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population. bioRxiv, 151068, ver. 3 of 12th November 2017. doi: 10.1101/151068
 Brown JKM, Chartrain L, Lasserre-Zuber P and Saintenac C. 2015. Genetics of resistance to Zymoseptoria tritici and applications to wheat breeding. Fungal Genetics and Biology, 79: 33–41. doi: 10.1016/j.fgb.2015.04.017
|Epidemiological trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population||Frederic Suffert, Henriette Goyeau, Ivan Sache, Florence Carpentier, Sandrine Gelisse, David Morais, Ghislain Delestre||The efficiency of plant resistance to fungal pathogen populations is expected to decrease over time, due to its evolution with an increase in the frequency of virulent or highly aggressive strains. This dynamics may differ depending on the scale i...||Adaptation, Evolutionary Applications, Evolutionary Epidemiology||Benoit Moury||2017-06-23 21:04:54||View|
11 Sep 2017
Less effective selection leads to larger genomesTristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N. Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando and Christophe Douady 10.1101/gr.212589.116
Colonisation of subterranean ecosystems leads to larger genome in waterlouse (Aselloidea)Recommended by Benoit Nabholz and Jochen B. W. Wolf
The total amount of DNA utilized to store hereditary information varies immensely among eukaryotic organisms. Single copy genome sizes – disregarding differences due to ploidy - differ by more than three orders of magnitude ranging from a few million nucleotides (Mb) to hundreds of billions (Gb). With the ever-increasing availability of fully sequenced genomes we now know that most of the difference is due either to whole genome duplication or to variation in the abundance of repetitive elements. Regarding repetitive elements, the evolutionary forces underlying the large variation 'allowing' more or less elements in a genome remain largely elusive. A tentative correlation between an organism's complexity (however this may be adequately measured) and genome size, the so called C-value paradox , has long been dismissed. Studies testing for selection on secondary phenotypic effects associated with genome size (cell size, metabolic rates, nutrient availability) have yielded mixed results. Nonadaptive theories capitalizing on a role of deleterious insertion-deletion mutations and genetic drift as the main drivers have likewise received mixed support [2-3]. Overall, most evidence was derived from analyses across broad taxonomical scales [4-6].
Lefébure and colleagues  take a different approach. They confine their considerations to a homogeneous, restricted taxonomical group, isopod crustaceans of the superfamily Aselloidea. This taxonomic focus allows the authors to circumvent many of the confounding factors such as phylogenetic inertia, life history divergence and mutation rate variation that tend to trouble analyses across broad taxonomic timescales. Another important feature of the chosen system is the evolutionary independent transition of habitat use that has occurred at least 11 times. One group of species inhabits subterranean ecosystems (groundwater), another group thrives on surface water. Populations of the former live in low-energy habitats and are expected to be outnumbered by their surface dwelling relatives. Interestingly – and a precondition for the study - the groundwater species have significantly larger genomes (up to 137%). With this unique set-up, the authors are able to investigate the link between genome size and evolutionary forces related to a proxy of long-term population size by removing many of the confounding factors a priori.
Upfront, we learn that the dN/dS ratio is higher in the groundwater species. This may either suggest prevalent positive selection or lower efficacy of purifying selection (relaxed constraint) in the group of species in which population sizes are expected to be low. Using a series of population genetic analyses the authors provide compelling evidence for the latter. Analyses are carefully conducted and include models for estimating the intensity and frequency of purifying and positive selection, the DoS (direction of selection) and α statistic. Next the authors also exclude the possibility that increased dN/dS of the subterranean groundwater species may be due to nonfunctionalization, which may result from the subterranean lifestyle.
Overall, these analyses suggest relaxed constraint in smaller populations as the most plausible alternative to explain increased dN/dS ratios. In addition to the efficacy of selection, the authors estimate the timing of the ecological transition under the rationale that the amount of time a species may have been exposed to the subterranean habitat may reflect long term population sizes. To calibrate the 'colonization clock' they apply a neat trick based on the degree of degeneration of the opsin gene (as vision tends to get lost in these habitats). When finally testing which parameters may explain differences in genome size all factors – ecological status, selection efficiency as measured by dN/dS and colonization time - turned out to be significant predictors. Direct estimates of the short term effective population size Ne from polymorphism data, however, did not correlate with genome size. Ruling out the effect of other co-variates such as body size and growth rate the authors conclude that genome size was overall best predicted by long-term population size change upon habitat shift. In that the authors provide convincing evidence that the increase in genome size is linked to a decrease in long-term reduction of selection efficiency of subterranean species. Assuming a bias for insertion mutations over deletion mutations (which is usually the case in eukaryotes) this result is in agreement with the theory of mutational hazard [4-6]. This theory proposed by Michael Lynch postulates that the accumulation of non-functional DNA has a weak deleterious effect that can only be efficiently opposed by natural selection in species with high Ne.
In conclusion, Lefébure and colleagues provide novel and welcome evidence supporting a 'neutralist' hypothesis of genome size evolution without the need to invoke an adaptive component. Methodologically, the study cautions against the common use of polymorphism-based estimates of Ne which are often obfuscated by transitory demographic change. Instead, alternative measures of selection efficacy linked to long-term population size may serve as better predictors of genome size. We hope that this study will stimulate additional work testing the link between Ne and genome size variation in other taxonomical groups [8-9]. Using genome sequences instead of the transcriptome approach applied here may concomitantly further our understanding of the molecular mechanisms underlying genome size change.
 Thomas, CA Jr. 1971. The genetic organization of chromosomes. Annual Review of Genetics 5: 237–256. doi: 10.1146/annurev.ge.05.120171.001321
 Ågren JA, Greiner S, Johnson MTJ, Wright SI. 2015. No evidence that sex and transposable elements drive genome size variation in evening primroses. Evolution 69: 1053–1062. doi: 10.1111/evo.12627
 Bast J, Schaefer I, Schwander T, Maraun M, Scheu S, Kraaijeveld K. 2016. No accumulation of transposable elements in asexual arthropods. Molecular Biology and Evolution 33: 697–706. doi: 10.1093/molbev/msv261
 Lynch M. 2007. The Origins of Genome Architecture. Sinauer Associates.
 Lynch M, Bobay LM, Catania F, Gout JF, Rho M. 2011. The repatterning of eukaryotic genomes by random genetic drift. Annual Review of Genomics and Human Genetics 12: 347–366. doi: 10.1146/annurev-genom-082410-101412
 Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302: 1401–1404. doi: 10.1126/science.1089370
 Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Der Sarkissian C, Charrier NP, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, and Douady CJ. 2017. Less effective selection leads to larger genomes. Genome Research 27: 1016-1028. doi: 10.1101/gr.212589.116
 Lower SS, Johnston JS, Stanger-Hall KF, Hjelmen CE, Hanrahan SJ, Korunes K, Hall D. 2017. Genome size in North American fireflies: Substantial variation likely driven by neutral processes. Genome Biolology and Evolution 9: 1499–1512. doi: 10.1093/gbe/evx097
 Sessegolo C, Burlet N, Haudry A. 2016. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biology Letters 12: 20160407. doi: 10.1098/rsbl.2016.0407
|Less effective selection leads to larger genomes||Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N. Pierre Charrier, David Eme, Florian Mermillod-Blondin, Lau...||The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However...||Evolutionary Theory, Genome Evolution, Molecular Evolution, Population Genetics / Genomics||Benoit Nabholz||2017-09-08 09:39:23||View|
Michael David Pirie
Alejandro Gonzalez Voyer