The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies.

Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

Nature-Based Solutions in the EU: Innovating with nature to address social, economic and environmental challenges.

Contemporary societies are facing a broad range of challenges, from pressures on human health and well-being to natural capital depletion, and the security of food, water and energy. These challenges are deeply intertwined with global processes, such as climate change and with local events such as natural disasters. The EU's research & innovation (R&I) policy is now seeking to address these challenges from a new perspective, with Nature-Based Solutions, and turn them into innovation opportunities that optimise the synergies between nature, society and the economy. Nature-Based Solutions can be an opportunity for innovation, and are here promoted by both policymakers and practitioners as a cost-effective way of creating a greener, more sustainable, and more competitive economy. Since 2013, the European Commission has devoted particular attention to Nature-Based Solutions through consultations and dialogues that sought to make the concept of these solutions more concrete and to define the concept's place within the spectrum of ecosystem-based approaches. In 2014, the Commission launched an expert group, which conducted further analysis, and made recommendations to help increase the use of Nature-Based Solutions and bring nature back into cities. In 2015, a survey was conducted on citizens' views and perceptions of 'Nature in Cities' to provide further insight for future work. Based on these elements and on results from running EU projects, the Commission has developed an R&I agenda for Nature-Based Solutions and has published targeted calls for proposals for large-scale demonstration projects in this field in 2016 and 2017. Additional R&I actions at EU level that promote systemic Nature-Based Solutions and their benefits to cities and territories are planned with the aim to improve the implementation capacity and evidence base for deploying Nature-Based Solutions and developing corresponding future markets. They are also expected to foster an interdisciplinary R&I and stakeholder community and the exchange of good practices in this field, as well as help shaping and implementing international R&I agendas on Nature-Based Solutions.

Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions.

BACKGROUND: Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. RESULTS: Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts. CONCLUSIONS: We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima's D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis.

Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies.

The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the "fast-X" or "fast-Z" effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes.

A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate.

Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.

Isolation of 12 microsatellite markers following a pyrosequencing procedure and cross-priming in two invasive cryptic species, Alexandrium catenella (group IV) and A. tamarense (group III) (Dinophyceae).

Alexandrium catenella (group IV) and Alexandrium tamarense (group III) (Dinophyceae) are two cryptic invasive phytoplankton species belonging to the A. tamarense species complex. Their worldwide spread is favored by the human activities, transportation and climate change. In order to describe their diversity in the Mediterranean Sea and understand their settlements and maintenances in this area, new microsatellite markers were developed based on Thau lagoon (France) samples of A. catenella and A. tamarense strains. In this study twelve new microsatellite markers are proposed. Five of these microsatellite markers show amplifications on A. tamarense and ten on A. catenella. Three of these 12 microsatellite markers allowed amplifications on both cryptic species. Finally, the haplotypic diversity ranged from 0.000 to 0.791 and 0.000 to 0.942 for A. catenella and A. tamarense respectively.

Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.

In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.

'Candidatus Ancillula trichonymphae', a novel lineage of endosymbiotic Actinobacteria in termite gut flagellates of the genus Trichonympha.

Termite gut flagellates are colonized by host-specific lineages of ectosymbiotic and endosymbiotic bacteria. Previous studies have shown that flagellates of the genus Trichonympha may harbour more than one type of symbiont. Using a comprehensive approach that combined cloning of SSU rRNA genes with fluorescence in situ hybridization and electron microscopy, we investigated the phylogeny and subcellular locations of the symbionts in a variety of Trichonympha species from different termites. The flagellates in Trichonympha Cluster I were the only species associated with 'Endomicrobia', which were located in the posterior part of the cell, confirming previous results. Trichonympha species of Cluster II from the termite genus Incisitermes (family Kalotermitidae) lacked 'Endomicrobia' and were associated with endosymbiotic Actinobacteria, which is highly unusual. The endosymbionts, for which we suggest the name 'Candidatus Ancillula trichonymphae', represent a novel, deep-branching lineage in the Micrococcineae that consists exclusively of clones from termite guts. They preferentially colonized the anterior part of the flagellate host and were highly abundant in all species of Trichonympha Cluster II except Trichonympha globulosa. Here, they were outnumbered by a Desulfovibrio species associated with the cytoplasmic lamellae at the anterior cell pole. Such symbionts are present in both Trichonympha clusters, but not in all species. Unlike the intracellular location reported for the Desulfovibrio symbionts of Trichonympha agilis (Cluster I), the Desulfovibrio symbionts of T. globulosa (Cluster II) were situated in deep invaginations of the plasma membrane that were clearly connected to the exterior of the host cell.

Osmoregulatory strategies in natural populations of the black-chinned tilapia Sarotherodon melanotheron exposed to extreme salinities in West African estuaries.

The effect of salinity was studied in natural populations of the black-chinned tilapia (Sarotherodon melanotheron) from West Africa. This euryhaline species colonizes nearly all coastal environments from bays to lagoons characterized by salinities ranging from fresh water to hypersaline water over 100 ‰. Individuals were sampled during the dry season at several locations characterized by different levels of salinity (3-102 ‰). Their osmotic status and their gills were analyzed. The branchial mitochondria-rich cells (MRC), localized at the basis of the filaments and along the lamellae in fish taken from the saline stations, showed a wide plasticity with significant differences in their number and size. The most striking results were a significant larger area (≈3x) and a higher number (≈55x) of MRC at high salinity (102 ‰) compared to low salinity (3 ‰). The major ion transporters and channels were localized by immunocytochemistry and different expression patterns have been recorded between stations. Despite an increased Na⁺/K⁺-ATPase (NKA) α-subunit expression and NKA activity, pointing to an increased monovalent ion excretion, a severe osmotic imbalance was recorded in animals living in hypersaline environments.

Putatively free-living 'Endomicrobia'- ancestors of the intracellular symbionts of termite gut flagellates?

Endomicrobia represent a candidate class in the Elusimicrobia phylum (formerly Termite Group 1) and were originally described as obligate intracellular symbionts of gut flagellates in lower termites. However, 16S rRNA gene sequences of Endomicrobia have been detected also in the gut of insects that do not possess such flagellates, e.g. higher termites and cockroaches. When we eliminated the large gut flagellates of Reticulitermes santonensis by feeding a starch diet, we discovered novel lineages of Endomicrobia that were hitherto undetected in normally faunated specimens. The new phylotypes are clearly separated from the endosymbionts of gut flagellates and fall into the radiation of those from flagellate-free insects. Comprehensive phylogenetic analysis documented that Endomicrobia comprise an apical cluster of endosymbionts that is not necessarily monophyletic and several apparently basal lineages that include bacteria present in the gut of defaunated lower termites, the naturally flagellate-free guts of higher termites and scarab beetle larvae, and in the cow rumen. We propose that these lineages represent hitherto undetected free-living Endomicrobia that share a common ancestor with the intracellular symbionts.