Lucie Vincenot

Tree-related microhabitats (TreMs) are widely used as indicators of structural complexity and biodiversity in temperate forests, yet the contribution of individual habitat trees to plot-level TreM diversity has not been quantified. Particularly, the role of Black Woodpecker (Dryocopus martius L.) cavity trees, which are considered key elements in close-to-nature forest practices, has rarely been examined. We combined an observational paired-plot design with a counterfactual approach to assess the magnitude and mechanisms by which Black Woodpecker cavity trees contribute to TreM diversity across a wide range of temperate forests in France, spanning from lowland and mountain sites. To isolate the specific contribution of the cavity tree, we constructed four counterfactual scenarios in which the Black Woodpecker cavity tree was either removed or replaced by alternative TreM-bearing trees. Observational comparisons showed that the plots containing a Black woodpecker cavity tree supported higher TreM alpha and gamma richness compared to control plots. Across all counterfactual scenarios, TreM alpha, beta and gamma diversities declined, meaning that no replacement strategy restored observed richness or composition of the Black Woodpecker cavity tree plot. Multivariate analysis revealed that the importance of the cavity tree is driven by saproxylic TreMs, reflecting the decay processes, excavation scars and secondary microhabitats. Our findings strengthen the importance of Black Woodpecker cavity trees as keystone habitat structures in managed forests and suggest that TreM-based biodiversity indicators and retention forestry guidelines should explicitly incorporate their presence.

Some plants abandoned photosynthesis and developed full dependency on fungi for nutrition. Most of the so-called mycoheterotrophic plants exhibit high specificity towards their fungal partners. We tested whether natural rarity of mycoheterotrophic plants and usual small and fluctuating population size make their populations more prone to genetic differentiation caused by restricted gene flow and/or genetic drift. We also tested whether these genetic characteristics might in turn shape divergent fungal preferences. We studied the mycoheterotrophic orchid Epipogium aphyllum, addressing the joint issues of genetic structure of its populations over Europe and possible consequences for mycorrhizal specificity within the associated fungal taxa. Out of 27 sampled E. aphyllum populations, nine were included for genetic diversity assessment using nine nuclear microsatellites and plastid DNA. Population genetic structure was inferred based on the total number of populations. Individuals from 17 locations were included into analysis of genetic identity of mycorrhizal fungi of E. aphyllum based on barcoding by nuclear ribosomal DNA. Epipogium aphyllum populations revealed high genetic diversity (uHe = 0.562) and low genetic differentiation over vast distances (F_ST = 0.106 for nuclear microsatellites and F_ST = 0.156 for plastid DNA). Bayesian clustering analyses identified only two genetic clusters, with a high degree of admixture. Epipogium aphyllum genets arise from panmixia and display locally variable, but relatively high production of ramets, as shown by a low value of rarefied genotypic richness (R_r = 0.265). Epipogium aphyllum genotype control over partner selection was negligible as (1) we found ramets from a single genetic individual associated with up to 68% of the known Inocybe spp. associating with the plant species, (2) and partner identity did not show any geographic structure. The absence of mosaicism in the mycorrhizal specificity over Europe may be linked to preferential allogamous habit of E. aphyllum and significant gene flow, which tend to promote host generalism.

The Asian knotweed species complex gathers some of the world’s most successful plant invaders including the Japanese knotweed (Reynoutria japonica), the giant knotweed (R. sachalinensis) and the hybrid of these two species, the Bohemian knotweed (R. × bohemica). Hybrid species often present higher competitive abilities compared to their parent species. While several studies have focused on the effects of knotweed invasion on plant communities, few have simultaneously considered (i) effects of the three taxa on native plant communities and (ii) effects on litter and soil faunal components. In this study, we compared the differential effects of three Asian knotweeds on vegetation and soil macroinvertebrates communities across seven sites on a regional scale in North Western France. All three knotweed species displayed similar negative effects on local plant species richness, while promoting the taxonomic richness of litter-dwelling macroinvertebrates. Belowground macroinvertebrate taxonomic richness appeared strongly reduced by the presence of the hybrid R. × bohemica, significantly more so than those of sites colonized by R. japonica or R. sachalinensis. These changes of belowground communities were correlated to associated changes of composition and richness within plant communities. This study provides new insight into the consequences of ecosystem invasion by these species, especially revealing the even further strength of impacts of the hybrid Bohemian knotweed on local vegetation and belowground macroinvertebrates than those of other Asian knotweeds, which points to the need for monitoring the spatial spread of R. × bohemica and describing further its effects on ecosystem properties.

Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic‐based experimental comparisons is required. In long‐lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo‐response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress‐response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long‐lived trees.

Global trade increases plant introductions, but joint introduction of associated microbes is overlooked. We analyzed the ectomycorrhizal fungi of a Caribbean beach tree, seagrape (Coccoloba uvifera, Polygonacaeae), introduced pantropically to stabilize coastal soils and produce edible fruits. Seagrape displays a limited symbiont diversity in the Caribbean. In five regions of introduction (Brazil, Japan, Malaysia, Réunion and Senegal), molecular barcoding showed that seagrape mostly or exclusively associates with Scleroderma species (Basidiomycota) that were hitherto only known from Caribbean seagrape stands. An unknown Scleroderma species dominates in Brazil, Japan and Malaysia, while Scleroderma bermudense exclusively occurs in Réunion and Senegal. Population genetics analysis of S. bermudense did not detect any demographic bottleneck associated with a possible founder effect, but fungal populations from regions where seagrape is introduced are little differentiated from the Caribbean ones, separated by thousands of kilometers, consistently with relatively recent introduction. Moreover, dry seagrape fruits carry Scleroderma spores, probably because, when drying on beach sand, they aggregate spores from the spore bank accumulated by semi-hypogeous Scleroderma sporocarps. Aggregated spores inoculate seedlings, and their abundance may limit the founder effect after seagrape introduction. This rare pseudo-vertical transmission of mycorrhizal fungi likely contributed to efficient and repeated seagrape/Scleroderma co-introductions.

Summary: Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long‐lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation‐by‐distance) and selective (isolation‐by‐adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present‐day patterns of genetic diversity.