Background: The maternally inherited bacteriumWolbachiaoften acts as a subtle parasite that manipulates insect reproduction, resulting potentially in reproductive isolation between host populations. Whilst distinctWolbachiastrains are documented in a group of evolutionarily closely related mosquitoes known as theCulex pipienscomplex, their impact on mosquito population genetics remains unclear. To this aim, we developed a PCR-RFLP test that discriminates the five knownWolbachiagroups found in this host complex. We further examined theWolbachiagenetic diversity, the variability in the coinherited host mitochondria and their partitioning among members of theCx. pipienscomplex, in order to assess the impact ofWolbachiaon host population structure.Results: There was a strong association betweenWolbachiaand mitochondrial haplotypes indicating a stable co-transmission in mosquito populations. Despite evidence that members of theCx. pipienscomplex are genetically distinct on the basis of nuclear DNA, the association ofWolbachiaand mtDNA with members of theCx. pipienscomplex were limited. TheWolbachia wPip-I group, by far the most common, was associated with divergentCx. pipiensmembers, includingCx. quinquefasciatus,Cx. pipiens pipiensformpipiensandCx. pipiens pipiensformmolestus. Four otherwPip groups were also found in mosquito populations and all were shared between diverseCx. pipiensmembers.Conclusion: This data overall supports the hypothesis thatwPip infections, and their allied mitochondria, are associated with regular transfers betweenCx. pipiensmembers rather than specific host associations. Overall, this is suggestive of a recent and likely ongoing cytoplasmic introgression through hybridization events across theCx. pipienscomplex.

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the ‘cost of complexity’ theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, N_e, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of N_e over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes.

Norway spruce (Picea abies) is a dominant conifer species of major economic importance in northern Europe. Extensive breeding programs were established to improve phenotypic traits of economic interest. In southern Sweden, seeds used to create progeny tests were collected on about 3,000 trees of outstanding phenotype (‘plus’ trees) across the region. In a companion paper, we showed that some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and bud‐burst) and assess the potential of assisted gene flow. Through a combination of multivariate analyses and genome‐wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (bud‐burst) with trees from southern origins outperforming local provenances. Association studies revealed that growth traits were highly polygenic and bud‐burst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help to alleviate the effect of climate change on P. abies breeding programs in Sweden.

Dose–response relationships reflect the effects of a substance on organisms, and are widely used in broad research areas, from medicine and physiology, to vector control and pest management in agronomy. Furthermore, reporting on the response of organisms to stressors is an essential component of many public policies (e.g. public health, environment), and assessment of xenobiotic responses is an integral part of World Health Organization recommendations. Building upon an R script that we previously made available, and considering its popularity, we have now developed a software package in the R environment,BioRssay, to efficiently analyze dose–response relationships. It has more user-friendly functions and more flexibility, and proposes an easy interpretation of the results. The functions in theBioRssaypackage are built on robust statistical analyses to compare the dose/exposure–response of various bioassays and effectively visualize them in probit-graphs.Graphical Abstract