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Additional file 1: Supplementary Figure S1. Results of CAFE analysis inferring the size change of gene families in the genome of nine tested Coleoptera species. This summary tree shows the number of expanded (red) and contracted (green) families. The species’ ultrametric tree was adapted from Mckenna et al. [6]. Abbreviations of the tested species are defined in Table 1. Table S3. Comparison of life history traits of Cryptolaemus montrouzieri subjected to different diet treatments and starvation. Means (± SE) within a column followed by the same letter are not significantly different (P > 0.05). Figure S2. Heatmap of adjusted P values (Q) in Gene Ontology (GO) enrichment analysis for the transcriptome comparisons of alternative diets versus the natural prey of C. montrouzieri larvae. C: Cellular component; F: Molecular function; P: Biological process. The number of background genes of each GO term is shown in brackets. Enrichment with Q

Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average > 99%) and sequencing depth (average > 247×). A comparison with partial Sanger sequences indicated an accuracy of > 99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.

Table S1. Estimates of h, number of haplotypes; s, number of segregating sites; π, nucleotide diversity; Tajima’s D value, substitution rate of each locus estimated based on the substitution rate for cytb and GenBank accession number for each mtDNA and nuclear locus of C. alexandrinus and C. dealbatus were provided. The substitution rate of each locus was calculated using the method in Li et al. (2010): the ratio of net genetic distance of each locus across ingroup–outgroup was calculated, compared with net distance of mitochondrial cytochrome b (cytb) and then multiplied by the substitution rate for cytb (0.0105 ± 0.0005 substitution/site/mya, Weir & Schluter 2008). Table S2. Estimates of pairwise FST for each microsatellite locus between C. alexandrinus and C. dealbatus, LD test result (same for both species), Na, number of alleles, Ho, observed heterozygosity and He, expected heterozygosity in each species. Table S3. PCR amplification protocols for three mtDNA, 16 nuclear exons and 22 microsatellite loci genotyped for C. alexandrinus and C. dealbatus. Table S4. Genetic differentiation between each pair of sampling localities of C. alexandrinus and C. dealbatus. Estimates were based on 1729 bp mtDNA (lower diagonal, ΦST) and 13 microsatellite loci (upper diagonal, FST). Values highlighted in red represent significant value after Bonferroni correction. Table S5 The morphological measurements of C. alexandrinus and C. dealbatus in different breeding sites along the Chinese coast, and Taiwan and Hainan Islands. Site reference number corresponds to numbers in Fig. 1 and Table 1. The number of sample size for each site (n), the mean value of measurements including bill and wing length, body mass and their respective standard deviations (SD) are given. Only DNA samples from a breeding site in Cangzhou were collected but not the measurement, the corresponding data is missing for this population. Mean and SD of bill length, wing length and body mass for each population. Measurement data of the site 3-Cangzhou was not collected. Table S6. Pearson’s correlation coefficients between pairwise of bioclimatic variables with the ranges of C. alexandrinus and C. dealbatus. Figure S1. Haplotype networks based on 80 individuals of 12 nuclear loci not shown in Fig. 2. C. alexandrinus (blue) and C. dealbatus (yellow). Figure S2. The Bayesian clustering analysis with STRUCTURE clearly suggested two genetic clusters corresponding to C. alexandrinus and C. dealbatus. Shown is the maximum value of the Delta K (Δ K) in posterior likelihood Ln P (X/K) over 10 runs per K of STRUCTURE. Figure S3. Niche of C. alexandrinus and C. dealbatus in climatic space from a principal component analysis (PCA-env). a) and b) show the niche characteristics of C. alexandrinus and C. dealbatus, respectively, along the first two axes of the PCA. Grey shading shows the density of the occurrences of the species by cell. The solid and dashed contour lines illustrate, respectively, 100 and 50% of the available (background) environment. c) The contribution of the variables on the first two axes of the PCA and the percentage of inertia explained by the two axes. d) Observed niche overlap D between the two ranges (bars with a diamond) and simulated niche overlaps (grey bars) on which tests of niche equivalency were calculated with 100 iterations. Figure S4. Differentiation in the stable isotope ratios among breeding sites (top-left: δ13C and bottom-left: δ15N) and between the two plovers (top-right: δ13C and bottom-right: δ15N). In all representation, C. alexandrinus marked in blue and C. dealbatus in yellow. Figure S5. (a) Newhybrid simulations failed to reliably detect simulated hybrid individuals. Real data of individuals with posterior density higher than 95% in STRUCTURE, and data of 5 simulated F1 and F2 individuals, and 10 back-cross individuals on each direction was used to imitate a situation when hybrids were the minority in the population. (b) Newhybrid results from real data are highly consistent with the STRUCTURE results. KP represents C. alexandrinus, WFP represents C. dealbatus, bx represents back-crosses. Appendix S1. Reconstruction of potential range shifts induced by climatic changes and inference of environmental niche overlap between the two-plover species, Charadrius alexandrinus and C. dealbatus. Appendix S2. Inference of interspecific diet overlap using stable-isotope analysis between the two plover species, Charadrius alexandrinus and C. dealbatus. (DOCX 530 kb)

Invasive species pose a major threat to biodiversity but provide an opportunity to describe the processes that lead to changes in a species' range. The bank vole (Myodes glareolus) is an invasive rodent that was introduced to Ireland in the early twentieth century. Given its continuing range expansion, the substantial empirical data on its spread thus far, and the absence of any eradication program, the bank vole in Ireland represents a unique model system for studying the mechanisms influencing the rate of range expansion in invasive small mammals. We described the invasion using a reaction-diffusion model informed by empirical data on life history traits and demographic parameters. We subsequently modelled the processes involved in its range expansion using a rule-based spatially explicit simulation. Habitat suitability interacted with density-dependent parameters to influence dispersal, most notably the density at which local populations started to donate emigrating individuals, the number of dispersing individuals and the direction of dispersal. Whilst local habitat variability influenced the rate of spread, on a larger scale the invasion resembled a simple reaction-diffusion process. Our results suggest a Type 1 range expansion where the rate of expansion is generally constant over time, but with some evidence for a lag period following introduction. We demonstrate that a two-parameter empirical model and a rule-based spatially explicit simulation are sufficient to accurately describe the invasion history of a species that exhibits a complex, density-dependent pattern of dispersal

Aim: The current volume of global trade has led to an unprecedented rate of biological invasions, causing severe problems to native ecosystems. The knowledge of species introduction routes and areas suitable for establishment is therefore an important step in preventing future invasions. The situation can be further exacerbated by climate change, which might alter the amount of environmentally suitable areas for establishment of invasive species. Here, we focus on three Arion slug species recently introduced to North America and Australia with potentially significant impact— A. ater, A. rufus and A. vulgaris. Location: Worldwide. Results: We combined interception records, molecular analyses and species distribution modelling to assess their introduction history and to predict which regions are at highest risk of future invasions. We found extensive sharing of mitochondrial haplotypes among continents in all three species. In concordance with the genetic analyses, interception records suggest that slugs were introduced to the USA and Australia primarily from France, the Netherlands and the UK, but also from other locations in North America. The models predicted climatically suitable regions for the three Arion species in several areas across the globe for which management actions can be targeted. Main conclusions: While the amount of regions with climatic conditions that would be suitable for slug establishment is predicted to slightly decrease under future scenarios, new suitable areas will also emerge. We therefore recommend that prevention efforts to limit new introductions should continue in order to protect vulnerable native ecosystems.

Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next-generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus , a steppic Southwestern-Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human-mediated land-use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.

Additional results not displayed in the main text

Additional results not displayed in the main text

The population structure and seasonal movements of alpine birds in Europe are still largely unknown. Species living in high mountains now face acute risks of habitat loss, range contractions and local extinction due to current and projected climate change. Therefore, a better understanding of the spatial structuring and exchange among populations of European mountain birds is important from both ecological and conservation points of view. The White-winged Snowfinch Montifringilla nivalis is one of the most characteristic passerines of alpine habitats in Europe. Despite the fact that its breeding nuclei are relatively well defined, we still know little about the species’ population structure and movements in Western Europe. By analysing two mitochondrial loci (cytochrome b and the control region) and stable isotopes of hydrogen (d2H), we assessed to what extent breeding populations of Whitewinged Snowfinches in the Cantabrian Mountains (CM), the Pyrenees and the Alps, and also a wintering population in the Eastern Pyrenees, function as a metapopulation. We first show the phylogenetic relationships of the Whitewinged Snowfinch (Montifringilla nivalis subsp. nivalis) within the Snowfinch complex. When assessing the population structure in Western Europe, most mitochondrial haplotypes were present in all breeding populations, but one was only found in the CM where it predominated. The most widespread haplotypes at the breeding grounds were found in the majority of the wintering individuals, but none of them showed the haplotype specific to the CM. We did not find differences in d2H for the primary feathers among breeding populations, but rectrices of individuals wintering in the Pyrenees had considerably lower d2H values: isotopic analysis could thus be useful to assign wintering birds to their Alpine breeding grounds. Further studies combining ringing and the analyses of intrinsic markers are an essential step in better appraising the species’ metapopulation dynamics and guiding conservation.

Arion vulgaris (syn. A. lusitanicus) is the most destructive pest slug in Europe. The species has been regarded a classic case of an ongoing biological invasion with negative economic and ecological impact in many European countries, but this status has recently been contested. In this study, we assessed mitochondrial and autosomal genetic diversity in populations of A. vulgaris across the entire distribution range in order to characterize its evolutionary history. Mitochondrial diversity in A. vulgaris was strongly reduced compared with the closely related and largely codistributed noninvasive species A. rufus and A. ater, indicating a very rapid spread of A. vulgaris through Europe. Autosomal diversity assessed in 632 individuals from 32 populations decreased towards eastern and northern Europe which is consistent with the reported expansion of the species towards these regions in the last decades. Demographic simulations supported very recent population founding events in most of the European range. The short periods between the first detection of A. vulgaris in different countries and only a very weak association of genetic structuring among populations with geographical distances suggest a human contribution in the ongoing expansion of the slug. We propose that this contribution may ultimately prevent the exact localization of the debated region of origin of A. vulgaris. However, the reclassification of A. vulgaris as noninvasive would be premature. Without counter measures, the Eastern and Northern European countries can expect to see this biological invasion continued in the future.

An understanding of the distribution and spatial structure of the natural vectors of zoonothic pathogens is of interest for effective disease control and prevention. Here, we investigate the range-wide population genetic structure of common pochard (Aythya ferina), a long-distance migratory duck and potential vector of highly pathogenic avian influenza. We collected several hundred samples from breeding and wintering grounds across Eurasia including some H5N1-positive individuals and generated partial sequences of the mitochondrial control region and multilocus microsatellite genotypes. Genetic differentiation among breeding populations was significant for both marker types but higher for maternally inherited mtDNA than for biparentally inherited nuclear markers. There was only weak genetic divergence between ducks sampled in Europe and East Asia, and genetic differentiation between populations was not generally associated with geographical distance. No evidence of genetic substructure was detected for ducks sampled on the European wintering grounds. Our results suggest limited breeding-site fidelity, especially in females, but extensive population admixture on the wintering grounds. The specific role of pochards as natural vectors of zoonotic pathogens and in particular H5N1 remains to be clarified but our results point to wintering grounds as potential hotspots for disease transmission.