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Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on FST and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating FST and genetic distances, and we compared this method with a new method proposed here (for FST only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, FST and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of FST and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. FST estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results. [PUBLICATION ABSTRACT]

Under environmental stress, previously hidden additive genetic variation can be unmasked and exposed to selection. The amount of hidden variation is expected to be higher for life history traits, which strongly correlate to individual fitness, than for morphological traits, in which fitness effects are more ambiguous. However, no consensual pattern has been recovered yet, and this idea is still debated in the literature. Here, we hypothesize that the classical categorization of traits (i.e., life history and morphology) may fail to capture their proximity to fitness. In the desert locust, Schistocerca gregaria, a model organism for the study of insect polyphenism, we quantified changes in additive genetic variation elicited by lifetime thermal stress for ten traits, in which evolutionary significance is known. Irrespective of their category, traits under strong stabilizing selection showed genetic invariance with environmental stress, while traits more loosely associated with fitness showed a marked increase in additive genetic variation in the stressful environment. Furthermore, traits involved in adaptive phenotypic plasticity (growth compensation) showed either no change in additive genetic variance or a change of moderate magnitude across thermal environments. We interpret this mitigated response of plastic traits in the context of integrated evolution to adjust the entire phenotype in heterogeneous environments (i.e., adaptiveness of initial plasticity, compromise of phenotypic compensation with stress, and shared developmental pathway). Altogether, our results indicate, in agreement with theoretical expectations, that environmental stress can increase available additive genetic variance in some desert locust traits, but those closely linked to fitness are largely unaffected. Our study also highlights the importance of assessing the proximity to fitness of a trait on a case‐by‐case basis and in an ecologically relevant context, as well as considering the processes of canalization and plasticity, involved in the control of phenotypic variation. The idea that environmental stress can unmask cryptic additive genetic variation and expose it to selection is well accepted. Still, no consensus has been reached on the potential magnitude of these stress‐induced changes. In the desert locust (Schistocerca gregaria), we show that ecologically relevant environmental stress increases available additive genetic variance only for traits that are not directly linked to individual fitness. Our results suggest that using a life history versus morphology categorization of traits as a proxy for their link to fitness might be too simplistic, and instead, traits' proximity to fitness should be known specifically in the studied populations. Our study also highlights that traits' control of phenotypic variation (canalization vs. plasticity) should not be overlooked.

Orthoptera are infected by about 60 species of gregarines assigned to the genus Gregarina Dufour, 1828. Among these species, Gregarina garnhami Canning, 1956 from Schistocerca gregaria (Forsskål, 1775) was considered by Lipa et al. in 1996 to be synonymous with Gregarina acridiorum (Léger 1893), a parasite of several orthopteran species including Locusta migratoria (Linné, 1758). Here, a morphological study and molecular analyses of the SSU rDNA marker demonstrate that specimens of S. gregaria and specimens of L. migratoria are infected by two distinct Gregarina species, G. garnhami and G. acridiorum, respectively. Validation of the species confirms that molecular analyses provide useful taxonomical information. Phenotypic plasticity was clearly observed in the case of G. garnhami : the morphology of its trophozoites, gamonts and syzygies varied according to the geographical location of S. gregaria and the subspecies infected. Les orthoptères sont parasités par environ soixante espèces de grégarines affiliées au genre Gregarina Dufour, 1828. Parmi ces espèces Gregarina garnhami Canning, 1956 décrite chez Schistocerca gregaria (Forskål, 1775), a été mise en synonymie par Lipa et al. en 1996 avec Gregarina acridiorum (Léger 1893), parasite de plusieurs espèces d’orthoptères dont Locusta migratoria (Linné, 1758). Ici, une étude morphologique et des analyses moléculaires du marqueur SSU rDNA démontrent que les spécimens de S. gregaria et ceux de L. migratoria sont infectés par 2 espèces distinctes de grégarines, Gregarina garnhami et Gregarina acridiorum , respectivement. La validation de ces espèces confirme l’importance des informations fournies par les analyses moléculaires dans les études taxonomiques. Une plasticité phénotypique a été clairement observée dans le cas de G. garnhami : la morphologie de ses trophozoïtes, gamontes et syzygies varie selon la localisation géographique et la sous-espèce de S. gregaria infectée.

Tychoparthenogenesis, a form of asexual reproduction in which a small proportion of unfertilized eggs can hatch spontaneously, could be an intermediate evolutionary link in the transition from sexual to parthenogenetic reproduction. The lower fitness of tychoparthenogenetic offspring could be due to either developmental constraints or to inbreeding depression in more homozygous individuals. We tested the hypothesis that in populations where inbreeding depression has been purged, tychoparthenogenesis may be less costly. To assess this hypothesis, we compared the impact of inbreeding and parthenogenetic treatments on eight life‐history traits (five measuring inbreeding depression and three measuring inbreeding avoidance) in four laboratory populations of the desert locust, Schistocerca gregaria, with contrasted demographic histories. Overall, we found no clear relationship between the population history (illustrated by the levels of genetic diversity or inbreeding) and inbreeding depression, or between inbreeding depression and parthenogenetic capacity. First, there was a general lack of inbreeding depression in every population, except in two populations for two traits. This pattern could not be explained by the purging of inbreeding load in the studied populations. Second, we observed large differences between populations in their capacity to reproduce through tychoparthenogenesis. Only the oldest laboratory population successfully produced parthenogenetic offspring. However, the level of inbreeding depression did not explain the differences in parthenogenetic success between all studied populations. Differences in development constraints may arise driven by random and selective processes between populations. The existence of parthenogenesis is still a question in evolution because of the advantages of sexual reproduction. Species, which exhibit occasional or accidental parthenogenesis (i.e., tychoparthenogenesis), such as the desert locust (Schistocerca gregaria), provide the opportunity to directly compare sexual and parthenogenetic reproduction. However, we found no clear relationship between the level of inbreeding, inbreeding depression, and parthenogenetic capacity suggesting that others selective or random processes may have to be taken into account.

Biotic interactions can modulate the responses of organisms to environmental stresses, including diet changes. Gut microbes have substantial effects on diverse ecological and evolutionary traits of their hosts, and microbial communities can be highly dynamic within and between individuals in space and time. Modulations of the gut microbiome composition and their potential role in the success of a species to maintain itself in a new environment have been poorly studied to date. Here we examine this question in a large wood-boring beetle Cacosceles newmannii (Cerambycidae), that was recently found thriving on a newly colonized host plant. Using 16S metabarcoding, we assessed the gut bacterial community composition of larvae collected in an infested field and in “common garden” conditions, fed under laboratory-controlled conditions on four either suspected or known hosts (sugarcane, tea tree, wattle, and eucalyptus). We analysed microbiome variation (i.e. diversity and differentiation), measured fitness-related larval growth, and studied host plant lignin and cellulose contents, since their degradation is especially challenging for wood-boring insects. We show that sugarcane seems to be a much more favourable host for larval growth. Bacterial diversity level was the highest in field-collected larvae, whereas lab-reared larvae fed on sugarcane showed a relatively low level of diversity but very specific bacterial variants. Bacterial communities were mainly dominated by Proteobacteria, but were significantly different between sugarcane-fed lab-reared larvae and any other hosts or field-collected larvae. We identified changes in the gut microbiome associated with different hosts over a short time frame, which support the hypothesis of a role of the microbiome in host switches.

In a context of unprecedented insect decline, it is critical to have reliable monitoring tools to measure species diversity and their dynamic at large-scales. High-throughput DNA-based identification methods, and particularly metabarcoding, were proposed as an effective way to reach this aim. However, these identification methods are subject to multiple technical limitations, resulting in unavoidable false-positive and false-negative species detection. Moreover, metabarcoding does not allow a reliable estimation of species abundance in a given sample, which is key to document and detect population declines or range shifts at large scales. To overcome these obstacles, we propose here a human-assisted molecular identification (HAMI) approach, a framework based on a combination of metabarcoding and image-based parataxonomic validation of outputs and recording of abundance. We assessed the advantages of using HAMI over the exclusive use of a metabarcoding approach by examining 492 mixed beetle samples from a biodiversity monitoring initiative conducted throughout France. On average, 23% of the species are missed when relying exclusively on metabarcoding, this percent being consistently higher in species-rich samples. Importantly, on average, 20% of the species identified by molecular-only approaches correspond to false positives linked to cross-sample contaminations or mis-identified barcode sequences in databases. The combination of molecular methodologies and parataxonomic validation in HAMI significantly reduces the intrinsic biases of metabarcoding and recovers reliable abundance data. This approach also enables users to engage in a virtuous circle of database improvement through the identification of specimens associated with missing or incorrectly assigned barcodes. As such, HAMI fills an important gap in the toolbox available for fast and reliable biodiversity monitoring at large scales.

The Crau Plain grasshopper, Prionotropis rhodanica Uvarov, 1923 (Orthoptera: Pamphagidae: Thrinchinae), is a rare grasshopper species endemic to the Crau Plain, a steppic habitat in France with unique floristic and faunistic communities. During recent decades, the area covered by these steppic grasslands has been highly reduced and fragmented due to the development of irrigation-based agriculture, roads, as well as industrial and military complexes. The restricted distribution, low population density and poor dispersal ability of P. rhodanica, combined with the destruction of its habitat, has led to the classification of this species as critically endangered in the IUCN Red List of Threatened Species. Decreases in habitat quality due to intensive grazing in the remnant grassland patches constitute an additional threat for P. rhodanica that can impact population dynamics at a relatively small-scale. In this work, we focused on a small area of about 3 km² occupied by one of the largest subpopulations observed in 2000-2001. We conducted a single-time snapshot intensive survey of grasshopper density and genetic variation at 11 microsatellite markers. We used a recent method, MAPI, to visualize the spatial genetic structure as a continuous surface and to determine, with the simultaneous use of spatial cross-correlograms, whether the normalized difference vegetation index, which informs on the balance between vegetation productivity and grazing intensity, can explain grasshopper population structure at such a fine scale. We found that both population density and gene flow were strongly and positively correlated to habitat quality (higher productivity of grasslands and/or lower sheep grazing). The spatial scales of interaction between these variables were estimated to be highly similar, in the range of 812-880 meters. This result suggests that P. rhodanica is very sensitive to the quality of the grasslands it inhabits.

Understanding dispersal ability in pest species is critical for both theoretical aspects of evolutionary and population biology and from a practical standpoint, such as implementing effective forecasting systems. The small brown planthopper (SBPH), Laodelphax striatellus (Fallén), is an economically important pest, but few data exist on its dispersal ability. Here, we used mitochondrial and nuclear markers to elucidate the population genetic structure of SBPH and of the parasitic bacterium Wolbachia throughout temperate and subtropical China. Our results showed that the SBPH populations in China lack significant differences in genetic structure, suggesting extensive gene flow. Multilocus sequence typing revealed that Wolbachia infection was systematic and due to the same strain ( w Stri) within and across populations. However, the mtDNA haplogroups had a nonrandom distribution across the sampling localities, which correlated to latitudinal and climatic gradients. We explain this mito-nuclear discordance as a result of historical population recolonization or mitochondria adaptation to climate.

We conducted a comparative population genetic analysis of levels of genetic variation and its geographical structuring in three closely related species of grasshopper that co-occur in the Mediterranean Basin: Calliptamus italicus, C. barbarus and C. wattenwylianus. In the western part of their distributions 5 populations of C. italicus, 13 of C. barbarus and 10 of C. wattenwylianus were sampled. Bootstrap re-sampling of populations and microsatellite loci within each species indicated a lower level of genetic diversity and higher level of genetic differentiation in C. barbarus, which is less of an outbreak pest species than either of the other Calliptamus species studied. This may be due to lower effective sizes of non-outbreak populations and/or lower gene flow among them. [PUBLICATION ABSTRACT]

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera, is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m, that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations.