Ivan Scotti

French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Ecologie des Forêts Méditerranéennes

Many plants undergo adaptation to fire. Yet, as global change is increasing fire frequency worldwide, our understanding of the genetics of adaptation to fire is still limited. We studied the genetic basis of serotiny (the ability to disseminate seeds exclusively after fire) in the widespread, pioneer Mediterranean conifer Pinus halepensis Mill., by...

Delivering material selected for breeding purposes into the wild in the context of sustainable forest management might reduce the levels of genetic diversity of future forests in comparison to that of natural populations. Another consequence might be a reduction of their resilience under uncertain future climatic and socio-economic conditions if th...

Past environmental changes have shaped the demographic history and genetic diversity of natural populations, yet the timescale and strength of these effects have not been investigated systematically and simultaneously for multiple phylogenetically distant species. We performed comparative population genomic analyses and demographic inference for se...

Microgeographic adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong selection is that underlies them, remain open questions. H...

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more...

When environmental conditions differ both within and among populations, multiscale adaptation results from processes at both scales and interference across scales. We hypothesize that within‐population environmental heterogeneity influences the chance of success of migration events, both within and among populations, and maintains within‐population...

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139...

In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight...

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139...

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecolog...

Motivation: Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait a...

Trees are characterized by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually, only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely...

Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees –whose large and undisturbed populations often span a variety of environmental conditions and local habitats – are particularly good models to study this process. Here, we...

The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite mar...

Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very o...

Devant l’inéluctable dépérissement de certaines espèces d’arbres, des chercheurs s’interrogentet étudient les capacités adaptatives des différentes essences

Fragmentation acting over geological times confers wide, biogeographical scale and genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a widespread forest tree, Pinus nigra Arnold, the European black pine, and to r...

Inter-individual variability of tree drought responses within a stand has received little attention. Here we explore whether the spatial variations in soil/subsoil properties assessed through electrical resistivity tomography (ERT) could explain variations in drought response traits among trees.  We used ERT to compute the percent variation in res...

• We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequ...

Fragmentation acting over geological times confers wide, biogeographical scale, genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a major European forest tree and to resolve its demographic history, we describe a...

Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees whose large and undisturbed populations often span a variety of environmental conditions and local habitats are particularly good models to study this process. Here, we ca...

Hylesia moths impact human health in South America, inducing epidemic outbreaks of lepidopterism, a puriginous dermatitis caused by the urticating properties of females’ abdominal setae. The classification of the Hylesia genus is complex, owing to its high diversity in Amazonia, high intraspecific morphological variance, and lack of interspecific d...

Plant populations are able to undergo very localized adaptive processes, that allow continuous populations to adapt to divergent habitats in spite of recurrent gene flow. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a nested sampling design, to evaluate microgeographi...

Although there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite the presence of genetic variation and selection pressures - theoretical prerequisites for the response to selection. This conundrum...

QST is a differentiation parameter based on the decomposition of the genetic variance of a trait. In the case of additive inheritance and absence of selection, it is analogous to the genic differentiation measured on individual loci, FST . Thus, QST - FST comparison is used to infer selection: selective divergence when QST > FST , or convergence wh...

How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rain fall and temperature changes during and/or immediately after the Last Glacial Maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil re...

How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rain fall and temperature changes during and/or immediately after the Last Glacial Maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil re...

Key message: Genetic diversity appears to be unaffected by disturbance in a stand of the light-demanding Neotropical treeV. michelii. Although spatial genetic structure is modified in post-disturbance cohorts, mixing of seeds from different mother trees in canopy gaps appears to efficiently maintain genetic admixture. Context: The interplay between...

Local adaptation is generally considered at a large geographic scale, due to the common idea that high gene flow at microgeographic scale (i.e. within dispersal neighborhood) should prevent sub-populations to evolve traits conferring them a better fitness in their micro-habitat. However, environmental heterogeneity within populations can be huge, a...

In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While genome-wide divergence is driven by neutral factors which affect the genome in a homogeneous manner, natural selection affects a reduced fraction of targeted genomic regions. This provides a conceptual framework for t...

Key message Forest disturbance affects the within-population distribution of genetic diversity, but not its overall levels, in a tropical pioneer tree species. In particular, clumps of related saplings with impoverished diversity are found in canopy gaps but not under forest cover. Context Forest disturbances can have long-term consequences on the...

Key messageThis review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology.ContextA decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving...

Background: In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adapti...

IntroductionDetermining the sources and role of intra-specific genetic variation is a classical focus of evolutionary biology (Mitchell-Olds et al. 2007). Ever since the beginning of population genetic studies in forest trees, the observation of high levels of within-stand phenotypic and, later, molecular diversity has been a commonplace. In these...

The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Vir...

Traditional measures of diversity, namely the number of species as well as Simpson's and Shannon's indices, are particular cases of Tsallis entropy. Entropy decomposition, i.e. decomposing gamma entropy into alpha and beta components, has been previously derived in the literature. We propose a generalization of the additive decomposition of Shannon...

Background and Aims In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics...

Context No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. Aims We developed a method to compare genome-wide diversity estimates while taking into...

Aim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression amo...

The phylogeographical history of Neotropical species can be difficult to reconstruct because of superimposed Neogene and Quaternary histories, and because of taxonomic uncertainty. We analysed range-wide genetic diversity in a widespread pioneer tree species, Jacaranda copaia (Aubl.) D. Don, to characterize phylogeographical structure, date the evo...

Unveiling the genetic basis of local adaptation to environmental variation is a major goal in molecular ecology. In rugged landscapes characterized by environmental mosaics, living populations and communities can experience steep ecological gradients over very short geographical distances. In lowland tropical forests, interspecific divergence in ed...

Communication orale + résumé

Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the step...

Description, amplification conditions and polymorphism of the nuclear simple sequence repeats (SSRs) analysed in Jacaranda copaia . (DOC)

Z-statistics and summary of Mantel tests for the correlations of pairs of genetic distance matrices within species. Colouring (shading) indicates the level of significance of the test: green (light grey*), P>0.05; orange (grey*), 0.05 0.001; red (dark grey*), P<0.001. Identity of DNA fragment sections is reported: simple sequence repeat (SSR) varia...

List and details of the sampled sites for the Jacaranda (J) data set. (DOC)

Complete alignments of DNA fragments for all SSR markers studied. Marker names are shown above each alignment. (PDF)

List and details of alleles for the three data sets. Amplicon sizes, frequencies and number of associated haplotypes are indicated for each allele. (DOC)

Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for s...

Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for s...

Mechanical signals have an impact on plant development. Tropical rainforest trees display large variability for life–history traits related to biomechanics and therefore are a unique study system to better understand biomechanical trait variability from an evolutionary perspective. From sequences and gene expression data available in model species,...

Recent evolutionary studies clearly indicate that evolution is mainly driven by changes in the complex mechanisms of gene regulation and not solely by polymorphism in protein-encoding genes themselves. After a short description of the cis-regulatory mechanism, we intend in this review to argue that by applying newly available technologies and by me...

Keywordsenvironmental change–evolution–adaptability–evolvability–plasticity

Evaluating the genetic architecture of sexual dimorphism can aid our understanding of the extent to which shared genetic control of trait variation versus sex-specific control impacts the evolutionary dynamics of phenotypic change within each sex. We performed a QTL analysis on Silene latifolia to evaluate the contribution of sex-specific QTL to ph...

Tropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; the...

Supplementary table S1. Neutral confidence intervals for mutation-drift equilibrium statistics as a function of rho for each Gene/population

Supplementary methods 1. (a) PCR and sequencing conditions for the isolation of gene sequences and (b) Conditions for Specific PCR amplifications.

Results of Bayesian estimation of total (true) population genetic variance. Mean mean value, sd standard deviation, lower, upper limit limits of the credible interval at 2.5% and 97.5%, respectively; median median value

Nineteen novel microsatellite loci were isolated from Adenomera andreae, a widespread Amazonian frog considered to be a species complex. Three multiplex kits were optimized. Genetic diversity was assessed in 66 individuals sampled in three populations along the West of the Approuague River catchment (French Guiana). We also tested the multiplex kit...

In rain forests, sapling survival is highly dependent on the regulation of trunk slenderness (height/diameter ratio): shade-intolerant species have to grow in height as fast as possible to reach the canopy but also have to withstand mechanical loadings (wind and their own weight) to avoid buckling. Recent studies suggest that mechanosensing is esse...

Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted...

Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangeme...

Quantitative genetic diversity is a fundamental component of the interaction between natural populations and their environment. In breeding programmes, quantitative genetic studies on tropical trees have so far focused on fast-growing, light-demanding species, but no information exists on shade-tolerant, slow-growing species. For this study, 27 3-y...