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Abstract Background Approximate Bayesian computation (ABC) is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populations. The software DIYABC offers a user-friendly interface allowing non-expert users to consider population histories involving any combination of population divergences, admixtures and population size changes. We here describe and illustrate new developments of this software that mainly include (i) inference from DNA sequence data in addition or separately to microsatellite data, (ii) the possibility to analyze five categories of loci considering balanced or non balanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii) the possibility to perform model checking computation to assess the "goodness-of-fit" of a model, a feature of ABC analysis that has been so far neglected. Results We used controlled simulated data sets generated under evolutionary scenarios involving various divergence and admixture events to evaluate the effect of mixing autosomal microsatellite, mtDNA and/or nuclear autosomal DNA sequence data on inferences. This evaluation included the comparison of competing scenarios and the quantification of their relative support, and the estimation of parameter posterior distributions under a given scenario. We also considered a set of scenarios often compared when making ABC inferences on the routes of introduction of invasive species to illustrate the interest of the new model checking option of DIYABC to assess model misfit. Conclusions Our new developments of the integrated software DIYABC should be particularly useful to make inference on complex evolutionary scenarios involving both recent and ancient historical events and using various types of molecular markers in diploid or haploid organisms. They offer a handy way for non-expert users to achieve model checking computation within an ABC framework, hence filling up a gap of ABC analysis. The software DIYABC V1.0 is freely available at http://www1.montpellier.inra.fr/CBGP/diyabc.

In an era of trade globalization and climate change, crop pathogens and pests are a genuine threat to food security. The detailed characterization of emerging pathogen populations is a prerequisite for managing invasive species pathways and designing sustainable disease control strategies. Huanglongbing is the disease that causes the most damage to citrus, a crop that ranks #1 worldwide in terms of fruit production. Huanglongbing can be caused by three species of the phloem-limited alpha-proteobacterium, " Candidatus Liberibacter," which are transmitted by psyllids. Two of these bacteria are of highest concern, " Ca . Liberibacter asiaticus" and " Ca . Liberibacter africanus," and have distinct thermal optima. These pathogens are unculturable, which complicates their high-throughput genetic characterization. In the present study, we used several genotyping techniques and an extensive sample collection to characterize Ca . Liberibacter populations associated with the emergence of huanglongbing in three French outermost regions of the European Union (Guadeloupe, Martinique and Réunion). The outbreaks were primarily caused by " Ca . Liberibacter asiaticus," as " Ca . Liberibacter africanus" was only found at a single location in Réunion. We emphasize the low diversity and high genetic relatedness between samples from Guadeloupe and Martinique, which suggests the putative movement of the pathogen between the two islands and/or the independent introduction of closely related strains. These samples were markedly different from the samples from Réunion, where the higher genetic diversity revealed by tandem-repeat markers suggests that the disease was probably overlooked for years before being officially identified in 2015. We show that " Ca . Liberibacter asiaticus" occurs from sea level to an altitude of 950 m above sea level and lacks spatial structure. This suggests the pathogen's medium- to long-distance movement. We also suggest that backyard trees acted as relays for disease spread. We discuss the implications of population biology data for surveillance and management of this threatful disease., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd.)

The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem ( Bothriochloa barbinodis ), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis -associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses., Competing Interests: In the interests of transparency and to help readers to form their own judgments of potential bias, the authors declare no competing interests in relation to the work described., (© The Author(s) 2024. Published by Oxford University Press.)

Theory generally predicts that host specialisation and dispersal should evolve jointly. Indeed, many models predict that specialists should be poor dispersers to avoid landing on unsuitable hosts while generalists will have high dispersal abilities. Phytophagous arthropods are an excellent group to test this prediction, given extensive variation in their host range and dispersal abilities. Here, we explore the degree to which the empirical literature on this group is in accordance with theoretical predictions. We first briefly outline the theoretical reasons to expect such a correlation. We then report empirical studies that measured both dispersal and the degree of specialisation in phytophagous arthropods. We find a correlation between dispersal and levels of specialisation in some studies, but with wide variation in this result. We then review theoretical attributes of species and environment that may blur this correlation, namely environmental grain, temporal heterogeneity, habitat selection, genetic architecture, and coevolution between plants and herbivores. We argue that theoretical models fail to account for important aspects, such as phenotypic plasticity and the impact of selective forces stemming from other biotic interactions, on both dispersal and specialisation. Next, we review empirical caveats in the study of this interplay. We find that studies use different measures of both dispersal and specialisation, hampering comparisons. Moreover, several studies do not provide independent measures of these two traits. Finally, variation in these traits may occur at scales that are not being considered. We conclude that this correlation is likely not to be expected from large-scale comparative analyses as it is highly context dependent and should not be considered in isolation from the factors that modulate it, such as environmental scale and heterogeneity, intrinsic traits or biotic interactions. A stronger crosstalk between theoretical and empirical studies is needed to understand better the prevalence and basis of the correlation between dispersal and specialisation., (© 2023 Cambridge Philosophical Society.)

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 × 10 -7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Côte d'Azur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations., (© 2023. The Author(s).)

One promising avenue for reconciling the goals of crop production and ecosystem preservation consists in the manipulation of beneficial biotic interactions, such as between insects and microbes. Insect gut microbiota can affect host fitness by contributing to development, host immunity, nutrition, or behavior. However, the determinants of gut microbiota composition and structure, including host phylogeny and host ecology, remain poorly known. Here, we used a well-studied community of eight sympatric fruit fly species to test the contributions of fly phylogeny, fly specialization, and fly sampling environment on the composition and structure of bacterial gut microbiota. Comprising both specialists and generalists, these species belong to five genera from to two tribes of the Tephritidae family. For each fly species, one field and one laboratory samples were studied. Bacterial inventories to the genus level were produced using 16S metabarcoding with the Oxford Nanopore Technology. Sample bacterial compositions were analyzed with recent network-based clustering techniques. Whereas gut microbiota were dominated by the Enterobacteriaceae family in all samples, microbial profiles varied across samples, mainly in relation to fly identity and sampling environment. Alpha diversity varied across samples and was higher in the Dacinae tribe than in the Ceratitinae tribe. Network analyses allowed grouping samples according to their microbial profiles. The resulting groups were very congruent with fly phylogeny, with a significant modulation of sampling environment, and with a very low impact of fly specialization. Such a strong imprint of host phylogeny in sympatric fly species, some of which share much of their host plants, suggests important control of fruit flies on their gut microbiota through vertical transmission and/or intense filtering of environmental bacteria., Competing Interests: The authors declare that there is no conflict of interest., (© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

The process of local adaptation involves differential changes in fitness over time across different environments. Although experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analysed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii., (© 2021 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.)

Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas . This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes ( CR , nd4 , and cytb ). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale., Competing Interests: None declared., (© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

A better understanding of the factors affecting host plant use by spotted-wing drosophila (Drosophila suzukii) could aid in the development of efficient management tools and practices to control this pest. Here, proxies of both preference (maternal oviposition behavior) and performance (adult emergence) were evaluated for 12 different fruits in the form of purees. The effect of the chemical composition of the fruits on preference and performance traits was then estimated. We synthesized the literature to interpret our findings in the light of previous studies that measured oviposition preference and larval performance of D. suzukii. We show that fruit identity influences different parts of the life cycle, including oviposition preference under both choice and no-choice conditions, emergence rate, development time, and number of emerging adults. Blackcurrant was always among the most preferred fruit we used, while grape and tomato were the least preferred fruits. Larvae performed better in cranberry, raspberry, strawberry, and cherry than in the other fruits tested. We found that fruit chemical compounds can explain part of the effect of fruit on D. suzukii traits. In particular, oviposition preference under choice conditions was strongly influenced by fruit phosphorus content. In general, the consensus across studies is that raspberry, blackberry, and strawberry are among the best hosts while blackcurrant, grape and rose hips are poor hosts. Our results generally confirm this view but also suggest that oviposition preferences do not necessarily match larval performances. We discuss opportunities to use our results to develop new approaches for pest management., (© The Author(s) 2019. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier , is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems. While the global and Indo-West Pacific population genetic structure of this species has recently been investigated, questions remain over population structure and demographic history within the western Indian (WIO) and within the western Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional population structures, the genetic diversity of 286 individuals sampled in seven localities was investigated using 27 microsatellite loci and three mitochondrial genes ( CR , COI, and cytb ). A weak genetic differentiation was observed between the WIO and the WPO, suggesting high genetic connectivity. This result agrees with previous studies and highlights the importance of the pelagic behavior of this species to ensure gene flow. Using approximate Bayesian computation to couple information from both nuclear and mitochondrial markers, evidence of a recent bottleneck in the Holocene (2,000-3,000 years ago) was found, which is the most probable cause for the low genetic diversity observed. A contemporary effective population size as low as 111 [43,369] was estimated during the bottleneck. Together, these results indicate low genetic diversity that may reflect a vulnerable population sensitive to regional pressures. Conservation measures are thus needed to protect a species that is classified as Near Threatened., Competing Interests: None declared.

Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections are key questions. The study of bacterial population biology can be challenging, because it requires high-resolution markers that can be genotyped with a high throughput. Here, we overcame this difficulty for Xanthomonas citri pv.  citri , a genetically monomorphic bacterium causing Asiatic citrus canker (ACC). Using a genotyping method that did not require cultivating the bacterium or purifying DNA, we deciphered the pathogen's spatial genetic structure at several microgeographic scales, down to single lesion, in a situation of ACC endemicity. In a grove where copper was recurrently applied for ACC management, copper-susceptible and copper-resistant X. citri pv.  citri coexisted and the bacterial population structured as three genetic clusters, suggesting a polyclonal contamination. The range of spatial dependency, estimated for the two largest clusters, was four times greater for the cluster predominantly composed of copper-resistant bacteria. Consistently, the evenness value calculated for this cluster was indicative of increased transmission. Linkage disequilibrium was high even at a tree scale, probably due to a combination of clonality and admixture. Approximately 1% of samples exhibited within-lesion multilocus polymorphism, explained at least in part by polyclonal infections. Canker lesions, which are of major biological significance as an inoculum source, may also represent a preferred niche for horizontal gene transfer. This study points out the potential of genotyping data for estimating the range of spatial dependency of plant bacterial pathogens, an important parameter for guiding disease management strategies., Competing Interests: None declared.

Predicting and managing contemporary adaption requires a proper understanding of the determinants of genetic variation. Spatial heterogeneity of the environment may stably maintain polymorphism when habitat contribution to the next generation can be considered independent of the degree of adaptation of local populations within habitats (i.e., under soft selection). In contrast, when habitats contribute proportionally to the mean fitness of the populations they host (hard selection), polymorphism is not expected to be maintained by selection. Although mathematically established decades ago, this prediction had never been demonstrated experimentally. Here, we provide an experimental test in which polymorphic populations of Escherichia coli growing in heterogeneous habitats were exposed to hard and soft selection regimes. As predicted by theory, polymorphism was preserved longer under soft selection. Complementary tests established that soft selection slowed fixation processes and could even protect polymorphism in the long term by providing a systematic advantage to rare genotypes., (© 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.)

The invasion of an established community by new species can trigger changes in community structure. Invasions often occur in phytophagous insect communities, the dynamics of which are driven by the structure of the host assemblage and the presence of competitors. In this study, we investigated how a community established through successive invasions changed over time, taking the last invasion as the reference. The community included four generalist and four specialist species of Tephritidae fruit flies. We analyzed a long-term database recording observed numbers of flies per fruit for each species on 36 host plants, over 18 years, from 1991 to 2009. Community structure before the last invasion by Bactrocera zonata in 2000 was described in relation to host plant phylogeny and resource availability. Changes in the host range of each species after the arrival of B .  zonata were then documented by calculating diversity indices. The flies in the community occupied three types of niches defined on the basis of plant phylogeny (generalists, Solanaceae specialist, and Cucurbitaceae specialists). After the arrival of B .  zonata , no change in the host range of specialist species was observed. However, the host ranges of two generalist species, Ceratitis quilicii and Ceratitis capitata , tended to shrink, as shown by the decreases in species richness and host plant α-diversity. Our study shows increased host specialization by generalist phytophagous insects in the field following the arrival of an invasive species sharing part of their resources. These findings could be used to improve predictions of new interactions between invaders and recipient communities.

Fungal plant parasites represent a growing concern for biodiversity and food security. Most ascomycete species are capable of producing different types of infectious spores both asexually and sexually. Yet the contributions of both types of spores to epidemiological dynamics have still to been fully researched. Here we studied the effect of mate limitation in parasites which perform both sexual and asexual reproduction in the same host. Since mate limitation implies positive density dependence at low population density, we modeled the dynamics of such species with both density-dependent (sexual) and density-independent (asexual) transmission rates. A first simple SIR model incorporating these two types of transmission from the infected compartment, suggested that combining sexual and asexual spore production can generate persistently cyclic epidemics in a significant part of the parameter space. It was then confirmed that cyclic persistence could occur in realistic situations by parameterizing a more detailed model fitting the biology of the Black Sigatoka disease of banana, for which literature data are available. We discuss the implications of these results for research on and management of Sigatoka diseases of banana.

Background: Phytophagous insects differ in their degree of specialisation on host plants, and range from strictly monophagous species that can develop on only one host plant to extremely polyphagous species that can develop on hundreds of plant species in many families. Nutritional compounds in host fruits affect several larval traits that may be related to adult fitness. In this study, we determined the relationship between fruit nutrient composition and the degree of host specialisation of seven of the eight tephritid species present in La Réunion; these species are known to have very different host ranges in natura. In the laboratory, larval survival, larval developmental time, and pupal weight were assessed on 22 fruit species occurring in La Réunion. In addition, data on fruit nutritional composition were obtained from existing databases., Results: For each tephritid, the three larval traits were significantly affected by fruit species and the effects of fruits on larval traits differed among tephritids. As expected, the polyphagous species Bactrocera zonata, Ceratitis catoirii, C. rosa, and C. capitata were able to survive on a larger range of fruits than the oligophagous species Zeugodacus cucurbitae, Dacus demmerezi, and Neoceratitis cyanescens. Pupal weight was positively correlated with larval survival and was negatively correlated with developmental time for polyphagous species. Canonical correspondence analysis of the relationship between fruit nutrient composition and tephritid survival showed that polyphagous species survived better than oligophagous ones in fruits containing higher concentrations of carbohydrate, fibre, and lipid., Conclusion: Nutrient composition of host fruit at least partly explains the suitability of host fruits for larvae. Completed with female preferences experiments these results will increase our understanding of factors affecting tephritid host range.

Background: Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands., Results: The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar., Conclusions: Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.

Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e., the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant-pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

Sexual reproduction and dispersal are often coupled in organisms mixing sexual and asexual reproduction, such as fungi. The aim of this study is to evaluate the impact of mate limitation on the spreading speed of fungal plant parasites. Starting from a simple model with two coupled partial differential equations, we take advantage of the fact that we are interested in the dynamics over large spatial and temporal scales to reduce the model to a single equation. We obtain a simple expression for speed of spread, accounting for both sexual and asexual reproduction. Taking Black Sigatoka disease of banana plants as a case study, the model prediction is in close agreement with the actual spreading speed (100 km per year), whereas a similar model without mate limitation predicts a wave speed one order of magnitude greater. We discuss the implications of these results to control parasites in which sexual reproduction and dispersal are intrinsically coupled.

In a cross-infection experiment, we investigated how seasonal changes can affect adaptation patterns in a Zymoseptoria tritici population. The fitness of isolates sampled on wheat leaves at the beginning and at the end of a field epidemic was assessed under environmental conditions (temperature and host stage) to which the local pathogen population was successively exposed. Isolates of the final population were more aggressive, and showed greater sporulation intensity under winter conditions and a shorter latency period (earlier sporulation) under spring conditions, than isolates of the initial population. These differences, complemented by lower between-genotype variability in the final population, exhibited an adaptation pattern with three striking features: (i) the pathogen responded synchronously to temperature and host stage conditions; (ii) the adaptation concerned two key fitness traits; (iii) adaptation to one trait (greater sporulation intensity) was expressed under winter conditions while, subsequently, adaptation to the other trait (shorter latency period) was expressed under spring conditions. This can be interpreted as the result of short-term selection, driven by abiotic and biotic factors. This case study cannot yet be generalized but suggests that seasonality may play an important role in shaping the variability of fitness traits. These results further raise the question of possible counterselection during the interepidemic period. While we did not find any trade-off between clonal multiplication on leaves during the epidemic period and clonal spore production on debris, we suggest that final populations could be counterselected by an Allee effect, mitigating the potential impact of seasonal selection on long-term dynamics., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Biological invaders have long been hypothesized to exhibit the fast end of the life-history spectrum, with early reproduction and a short lifespan. Here, we examine the rapid evolution of life history within the harlequin ladybird Harmonia axyridis. The species, once used as a biological control agent, is now a worldwide invader. We show that biocontrol populations have evolved a classic fast life history during their maintenance in laboratories. Invasive populations also reproduce earlier than native populations, but later than biocontrol ones. Invaders allocate more resources to reproduction than native and biocontrol individuals, and their reproduction is spread over a longer lifespan. This life history is best described as a bet-hedging strategy. We assert that invasiveness cannot be explained only by invoking faster life histories. Instead, the evolution of life history within invasive populations can progress rapidly and converge to a fine-tuned evolutionary match between the invaded environment and the invader.

Investigating the population biology of plant pathogens in their native areas is essential to understand the factors that shape their population structure and favour their spread. Monomorphic pathogens dispatch extremely low genetic diversity in invaded areas, and native areas constitute a major reservoir for future emerging strains. One of these, the gammaproteobacterium Xanthomonas citri pv. citri, causes Asiatic canker and is a considerable threat to citrus worldwide. We studied its population genetic structure by genotyping 555 strains from 12 Vietnam provinces at 14 tandem repeat loci and insertion sequences. Discriminant analysis of principal components identified six clusters. Five of them were composed of endemic strains distributed heterogeneously across sampled provinces. A sixth cluster, VN6, displayed a much lower diversity and a clonal expansion structure, suggesting recent epidemic spread. No differences in aggressiveness on citrus or resistance to bactericides were detected between VN6 and other strains. VN6 likely represents a case of bioinvasion following introduction in a native area likely through contaminated plant propagative material. Highly polymorphic markers are useful for revealing migration patterns of recently introduced populations of a monomorphic bacterial plant pathogen., (© 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.)

MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).

Cyclic parthenogens alternate asexual reproduction with periodic episodes of sexual reproduction. Sexually produced free-living forms are often their only way to survive unfavorable periods. When sexual reproduction requires the mating of two self-incompatible individuals, mating limitation may generate an Allee effect, which makes small populations particularly vulnerable to extinction; parthenogenetic reproduction can attenuate this effect. However, asexual reproduction likely trades off with sexual reproduction. To explore the evolutionary implications of such a trade-off, we included recurrent mating events associated with seasonal interruptions in a simple population dynamics model. Following an adaptive dynamics approach, we showed that positive density dependence associated with Allee effects in cyclic parthenogens promotes evolutionary divergence in the level of investment in asexual reproduction. Although polymorphism may be transient, morphs mostly investing into sexual reproduction may eventually exclude those predominantly reproducing in an asexual manner. Asexual morphs can be seen as making cooperative investments into the common pool of mates, while sexual morphs defect, survive better, and may eventually fix in the population. Our findings provide a novel hypothesis for the frequent coexistence of sexual and asexual lineages, notably in plant parasitic fungi.

Frequent and devastating epidemics of parasites are one of the major issues encountered by modern agriculture. To manage the impact of pathogens, resistant plant varieties have been selected. However, resistances are overcome by parasites requiring the use of pesticides and causing new economical and food safety issues. A promising strategy to maintain the epidemic at a low level and hamper pathogen's adaptation to varietal resistance is the use of mixtures of varieties such that the mix will form a heterogeneous environment for the parasite. A way to find the good combination of varieties that will actually constitute a heterogeneous environment for pathogens is to look for genotype × genotype (G × G) interactions between pathogens and plant varieties. A pattern in which pathogens have a high fitness on one variety and a poor fitness on other varieties guarantees the efficiency of the mixture strategy. In the present article, we inoculated 18 different genotypes of the fungus Magnaporthe oryzae on three rice plant varieties showing different levels of partial resistance in order to find a variety combination compatible with the requirements of the variety mixture strategy, i.e., showing appropriate G × G interactions. We estimated the success of each plant-fungus interaction by measuring fungal fitness and three fungal life history traits: infection success, within-host growth, sporulation capacity. Our results show the existence of G × G interactions between the two varieties Ariete and CO39 on all measured traits and fungal fitness. We also observed that these varieties have different resistance mechanisms; Ariete is good at controlling infection success of the parasite but is not able to control its growth when inside the leaf, while CO39 shows the opposite pattern. We also found that Maratelli's resistance has been eroded. Finally, correlation analyses demonstrated that not all infectious traits are positively correlated.

Dispersal is a key factor in invasion and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of the parent-offspring distance distribution, of the western corn rootworm, Diabrotica virgifera virgifera, one of the most destructive pests of maize. This species is currently invading Europe, and the two largest invasive outbreaks, in northern Italy and Central Europe, have recently formed a secondary contact zone in northern Italy. We identified vanishing clines at 12 microsatellite loci throughout the contact zone. By analysing both the rate of change of cline slope and the spatial variation of linkage disequilibrium at these markers, we obtained two σ estimates of about 20 km/generation(1/2). Simulations indicated that these estimates were robust to changes in dispersal kernels and differences in population density between the two outbreaks, despite a systematic weak bias. These estimates are consistent with the results of direct methods for measuring dispersal applied to the same species. We conclude that secondary contact resulting from multiple introductions is very useful for the inference of dispersal parameters and should be more widely used in other species., (© 2013 John Wiley & Sons Ltd.)

Sexual reproduction may be cryptic or facultative in fungi and therefore difficult to detect. Magnaporthe oryzae, which causes blast, the most damaging fungal disease of rice, is thought to originate from southeast Asia. It reproduces asexually in all rice-growing regions. Sexual reproduction has been suspected in limited areas of southeast Asia, but has never been demonstrated in contemporary populations. We characterized several M. oryzae populations worldwide both biologically and genetically, to identify candidate populations for sexual reproduction. The sexual cycle of M. oryzae requires two strains of opposite mating types, at least one of which is female-fertile, to come into contact. In one Chinese population, the two mating types were found to be present at similar frequencies and almost all strains were female-fertile. Compatible strains from this population completed the sexual cycle in vitro and produced viable progenies. Genotypic richness and linkage disequilibrium data also supported the existence of sexual reproduction in this population. We resampled this population the following year, and the data obtained confirmed the presence of all the biological and genetic characteristics of sexual reproduction. In particular, a considerable genetic reshuffling of alleles was observed between the 2 years. Computer simulations confirmed that the observed genetic characteristics were unlikely to have arisen in the absence of recombination. We therefore concluded that a contemporary population of M. oryzae, pathogenic on rice, reproduces sexually in natura in southeast Asia. Our findings provide evidence for the loss of sexual reproduction by a fungal plant pathogen outside its centre of origin., (© 2012 Blackwell Publishing Ltd.)

Adaptive evolution is currently accepted as playing a significant role in biological invasions. Adaptations relevant to invasions are typically thought to occur either recently within the introduced range, as an evolutionary response to novel selection regimes, or within the native range, because of long-term adaptation to the local environment. We propose that recent adaptation within the native range, in particular adaptations to human-altered habitat, could also contribute to the evolution of invasive populations. Populations adapted to human-altered habitats in the native range are likely to increase in abundance within areas frequented by humans and associated with human transport mechanisms, thus enhancing the likelihood of transport to a novel range. Given that habitats are altered by humans in similar ways worldwide, as evidenced by global environmental homogenization, propagules from populations adapted to human-altered habitats in the native range should perform well within similarly human-altered habitats in the novel range. We label this scenario 'Anthropogenically Induced Adaptation to Invade'. We illustrate how it differs from other evolutionary processes that may occur during invasions, and how it can help explain accelerating rates of invasions.

We derive a comprehensive overview of specialization evolution based on analytical results and numerical illustrations. We study the separate and joint evolution of two critical facets of specialization-local adaptation and habitat choice-under different life cycles, modes of density regulation, variance-covariance structures, and trade-off strengths. A particular feature of our analysis is the investigation of arbitrary trade-off functions. We find that local-adaptation evolution qualitatively changes the outcome of habitat-choice evolution under a wide range of conditions. In addition, habitat-choice evolution qualitatively and invariably changes the outcomes of local-adaptation evolution whenever trade-offs are weak. Even weak trade-offs, which favor generalists when habitat choice is fixed, select for specialists once local adaptation and habitat choice are both allowed to evolve. Unless trapped by maladaptive genetic constraints, joint evolution of local adaptation and habitat choice in the models analyzed here thus always leads to specialists, independent of life cycle, density regulation, and trade-off strength, thus raising the bar for evolutionarily sound explanations of generalism. Whether a single specialist or two specialists evolve depends on the life cycle and the mode of density regulation. Finally, we explain why the gradual evolutionary emergence of coexisting specialists requires more restrictive conditions than does their evolutionarily stable maintenance.

Because it increases relatedness between interacting individuals, population viscosity has been proposed to favour the evolution of altruistic helping. However, because it increases local competition between relatives, population viscosity may also act as a brake for the evolution of helping behaviours. In simple models, the kin selected fecundity benefits of helping are exactly cancelled out by the cost of increased competition between relatives when helping occurs after dispersal. This result has lead to the widespread view, especially among people working with social organisms, that special conditions are required for the evolution of altruism. Here, we re-examine this result by constructing a simple population genetic model where we analyse whether the evolution of a sterile worker caste (i.e. an extreme case of altruism) can be selected for by limited dispersal. We show that a sterile worker caste can be selected for even under the simplest life-cycle assumptions. This has relevant consequences for our understanding of the evolution of altruism in social organisms, as many social insects are characterized by limited dispersal and significant genetic population structure.

In plants, genes may disperse through both pollen and seeds. Here we provide a first theoretical study of the mechanisms and consequences of the joint evolution of pollen and seed dispersal. We focus on hermaphroditic self-compatible species distributed in structured populations, assuming island dispersal of pollen and seeds among small patches of plants within large populations. Three traits are studied: the rate of among-patch seed dispersal, the rate of among-patch pollen dispersal, and the rate of within-patch pollen movement. We first analytically derive the evolutionary equilibrium state of each trait, dissect the pairwise selective interactions, and describe the joint three-trait evolutionary equilibrium under the cost of dispersal and kin competition. These results are then analytically and numerically extended to the case when selfed seeds suffer from depressed competitiveness (inbreeding depression, no heterosis). Finally individual-based simulations are used to account for a more realistic model of inbreeding load. Pollen movement is shown to generate opposite selection pressures on seed dispersal depending on spatial scale: within-patch pollen movement favors seed dispersal, whereas among-patch pollen dispersal inhibits seed dispersal. Seed dispersal selects for short-distance movements of pollen and it selects against long-distance dispersal. These interactions shape the joint evolution of these traits. Kin competition favors among-patch seed dispersal over among-patch pollen dispersal for low costs of within-patch pollen movement (and vice versa for significant costs of within-patch pollen movement). Inbreeding depression favors allogamy through high rates of within- and among-patch pollen movement. Surprisingly, it may select either for or against seed dispersal depending on the cost of among-patch pollen dispersal. Heterosis favors increased among-patch dispersal through pollen and seeds. But because these two stages inhibit each other, their joint evolution might lead to decreased seed dispersal in the presence of heterosis. Of crucial importance are the costs of dispersal.

A large number of mathematical models have been developed that show how natural and sexual selection can cause prezygotic isolation to evolve. This article attempts to unify this literature by identifying five major elements that determine the outcome of speciation caused by selection: a form of disruptive selection, a form of isolating mechanism (assortment or a mating preference), a way to transmit the force of disruptive selection to the isolating mechanism (direct selection or indirect selection), a genetic basis for increased isolation (a one- or two-allele mechanism), and an initial condition (high or low initial divergence). We show that the geographical context of speciation (allopatry vs. sympatry) can be viewed as a form of assortative mating. These five elements appear to operate largely independently of each other and can be used to make generalizations about when speciation is most likely to happen. This provides a framework for interpreting results from laboratory experiments, which are found to agree generally with theoretical predictions about conditions that are favorable to the evolution of prezygotic isolation.