Topography drives microgeographic adaptations of closely related species in two tropical tree species complexes

Wet Season Environments Drive Local Adaptation in the Timber Tree Dicorynia guianensis in French Guiana

The vast tropical rainforests of the Guiana Shield in Northern South America play a vital role in maintaining the region's ecological balance and economy. Increasing pressure from selective logging, gold mining and climate variability threatens these ecosystems. Sustainable rainforest management requires understanding the genetic diversity and local adaptation of key tree species to inform conservation. This study focuses on Dicorynia guianensis (Fabaceae), a widespread and economically important tree species in French Guiana. We performed genome resequencing on 87 individuals sampled in 11 sites across French Guiana to investigate the genetic structure, diversity and genetic basis of local adaptation. Genetic structure analysis identified three distinct groups: western, central and eastern, with similar levels of genetic diversity distributed in areas with different environmental conditions. Six methods applied to detect genomic signatures of selection revealed region-specific selective sweeps and a weak overlap between single nucleotide polymorphisms (SNPs) identified through outlier analysis or genome-environment association analyses. The strongest associations between environmental variables and genomic constitution were observed for potential evapotranspiration of the wettest quarter and for precipitation of the coldest quarter, suggesting that environmental variables related to high rainfall during the wet season are stronger drivers of local adaptation of D. guianensis populations than drought. Sites located in central and western French Guiana had higher risks of climatic maladaptation. These findings advance our understanding of local adaptation and climatic vulnerability in tropical trees and emphasise the need for targeted, area-specific management strategies for conservation and sustainable timber extraction under climate change.

Selection in space and time: Individual tree growth is adapted to tropical forest gap dynamics

Tropical forest dynamics are driven by growth and survival strategies of tree species in relation to treefall gaps; however, the ecological and evolutionary roles of intraspecific variation in the response to forest gaps remain unexplored. Here, we associated genomic data of three related tree species of the genus Symphonia in a French Guiana forest with (1) each individual tree's growth potential, and (2) with its light and competition environment estimated based on 33 years of forest monitoring in plots covering 120 ha. We show that individual trees within species have genetically determined growth strategies that are adapted to the local light and competition environments, which are shaped by the time since the last treefall. Within species, fast-growing genotypes are more frequent in light-enriched environments and slow-growing genotypes in more shaded environments. Forest gap dynamics is thus a strong selection driver that shapes adaptive strategies and maintains genetic variation within tropical tree species.

Mind the lag: understanding genetic extinction debt for conservation

The delay between disturbance events and genetic responses within populations is a common but surprisingly overlooked phenomenon in ecology and evolutionary and conservation genetics. If not accounted for when interpreting genetic data, this time lag problem can lead to erroneous conservation assessments. We (i) identify life-history traits related to longevity and reproductive strategies as the main determinants of time lags, (ii) evaluate potential confounding factors affecting genetic parameters during time lags, and (iii) propose approaches that allow controlling for time lags. Considering the current unprecedented rate of loss of genetic diversity and adaptive potential, we expect our novel interpretive and methodological framework for time lags to stimulate further research and discussion on the most appropriate approaches to analyse genetic diversity for conservation.

Integrated effects of neighbourhood composition and resource levels on growth of a dominant tree species in a tropical forest

Abiotic environments and biotic neighbourhoods interact to influence plant growth and community assembly. However, the nature of this interaction depends very much on how biotic neighbourhoods are measured, including their relatedness to focal plants. In a tropical seasonal rainforest, we examine the growth of a dominant canopy species in response to environmental factors, the densities and relatedness of conspecific and heterospecific neighbours, and their interactions. We find significant environmental effects and conspecific negative density dependence on growth. Furthermore, conspecific neighbour density has stronger negative effects on growth under high light and soil water resource levels, but weaker negative effects under low light and soil water resource levels. In addition, more closely related heterospecifics in the neighbourhood have negative effects on growth under high soil phosphorus availability, but positive effects under low soil phosphorus availability. In contrast, more closely related conspecifics in the neighbourhood have negative effects on growth under low soil potassium availability, but positive effects under high soil potassium availability. Our study emphasizes the importance of both intra- and interspecific neighbourhood composition and their interactions with resource levels for understanding tree growth. This enhances our understanding of the complex processes in community assembly and species coexistence within forest communities.

Fine-Scale Variation in Soil Properties Promotes Local Taxonomic Diversity of Hybridizing Oak Species (Quercus spp.)

Although many tree species frequently hybridize and backcross, management decisions in forestry and nature conservation are usually concentrated on pure species. Therefore, understanding which environmental factors drive the distribution and admixture of tree species on a local stand scale is of great interest to support decision-making in the establishment and management of resilient forests. Here, we extensively sampled a mixed stand of hybridizing white oaks (Quercus petraea and Q. pubescens) near Lake Neuchâtel (Switzerland), where limestone and glacier moraine geologies coexist in proximity, to test whether micro-environmental conditions can predict taxonomic distribution and genetic admixture. We collected DNA from bud tissue, individual soil samples, and extracted high-resolution topographic data for 385 oak trees. We used 50 species-discriminatory single nucleotide polymorphism (SNP) markers to determine the taxonomic composition and admixture levels of individual trees and tested their association with micro-environmental conditions. We show that the trees' taxonomic distribution can be explained mainly by geographic position, soil pH, and potential rooting depth, a proxy for soil water availability. We found that admixed individuals tend to grow in habitats that are characteristic of the more drought-tolerant species Q. pubescens rather than in intermediate habitats. Using in situ measurements, we are the first to show that fine-scale variation in soil properties related to pH and water availability potentially drives the distribution of hybridizing tree species in a mixed stand. Microenvironmental variation therefore promotes local taxonomic diversity, facilitates admixture and adaptive introgression, and contributes to the resilience of forests under environmental change. Consequently, species such as white oaks should be managed and protected as a species complex rather than as pure species.

Demography-driven and adaptive introgression in a hybrid zone of the Armeria syngameon

Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune-adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range-edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt-exposed habitats.

Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets

Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.

High intraspecific growth variability despite strong evolutionary legacy in an Amazonian forest

Tree growth is key to species performance. However, individual growth variability within species remains underexplored for a whole community, and the role of species evolutionary legacy and local environments remains unquantified. Based on 36 years of diameter records for 7961 trees from 138 species, we assessed individual growth across an Amazonian forest. We related individual growth to taxonomy, topography and neighbourhood, before exploring species growth link to functional traits and distribution along the phylogeny. We found most variation in growth among individuals within species, even though taxonomy explained a third of the variation. Species growth was phylogenetically conserved up to the genus. Traits of roots, wood and leaves were good predictors of growth, suggesting their joint selection during convergent evolutions. Neighbourhood crowding significantly decreased individual growth, although much of inter-individual variation remains unexplained. The high intraspecific variation observed could allow individuals to respond to the heterogeneous environments of Amazonian forests.

Higher local intra- than interspecific variability in water- and carbon-related leaf traits among Neotropical tree species

BACKGROUND AND AIMS

Intraspecific variability in leaf water-related traits remains little explored despite its potential importance in the context of increasing drought frequency and severity. Studies comparing intra- and interspecific variability of leaf traits often rely on inappropriate sampling designs that result in non-robust estimates, mainly owing to an excess of the species/individual ratio in community ecology or, on the contrary, to an excess of the individual/species ratio in population ecology.

METHODS

We carried out virtual testing of three strategies to compare intra- and interspecific trait variability. Guided by the results of our simulations, we carried out field sampling. We measured nine traits related to leaf water and carbon acquisition in 100 individuals from ten Neotropical tree species. We also assessed trait variation among leaves within individuals and among measurements within leaves to control for sources of intraspecific trait variability.

KEY RESULTS

The most robust sampling, based on the same number of species and individuals per species, revealed higher intraspecific variability than previously recognized, higher for carbon-related traits (47-92 and 4-33 % of relative and absolute variation, respectively) than for water-related traits (47-60 and 14-44 % of relative and absolute variation, respectively), which remained non-negligible. Nevertheless, part of the intraspecific trait variability was explained by variation of leaves within individuals (12-100 % of relative variation) or measurement variations within leaf (0-19 % of relative variation) and not only by individual ontogenetic stages and environmental conditions.

CONCLUSIONS

We conclude that robust sampling, based on the same number of species and individuals per species, is needed to explore global or local variation in leaf water- and carbon-related traits within and among tree species, because our study revealed higher intraspecific variation than previously recognized.

Rethinking the nature of intraspecific variability and its consequences on species coexistence

Intraspecific variability (IV) has been proposed to explain species coexistence in diverse communities. Assuming, sometimes implicitly, that conspecific individuals can perform differently in the same environment and that IV increases niche overlap, previous studies have found contrasting results regarding the effect of IV on species coexistence. We aim at showing that the large IV observed in data does not mean that conspecific individuals are necessarily different in their response to the environment and that the role of high-dimensional environmental variation in determining IV has largely remained unexplored in forest plant communities. We first used a simulation experiment where an individual attribute is derived from a high-dimensional model, representing "perfect knowledge" of individual response to the environment, to illustrate how large observed IV can result from "imperfect knowledge" of the environment. Second, using growth data from clonal Eucalyptus plantations in Brazil, we estimated a major contribution of the environment in determining individual growth. Third, using tree growth data from long-term tropical forest inventories in French Guiana, Panama and India, we showed that tree growth in tropical forests is structured spatially and that despite a large observed IV at the population level, conspecific individuals perform more similarly locally than compared with heterospecific individuals. As the number of environmental dimensions that are well quantified at fine scale is generally lower than the actual number of dimensions influencing individual attributes, a great part of observed IV might be represented as random variation across individuals when in fact it is environmentally driven. This mis-representation has important consequences for inference about community dynamics. We emphasize that observed IV does not necessarily impact species coexistence per se but can reveal species response to high-dimensional environment, which is consistent with niche theory and the observation of the many differences between species in nature.

Seasonal variation of leaf thickness: An overlooked component of functional trait variability

The dry and wet seasons in the Neotropics have strong effects on soil water and nutrient availability, as well as on forest dynamics. Despite these major effects on forest ecology, little is known on how leaf traits vary throughout the seasons in tropical rainforest trees. Here, we investigated the influence of seasonal variations in climate and soil characteristics on leaf trait variation in two tropical tree species. We measured two leaf traits, thickness and water mass per area, in 401 individuals of two species of Symphonia (Clusiaceae) in the Paracou research station in French Guiana tropical lowland rainforest. We found a significant effect of seasonal variation on these two leaf traits. Soil relative extractable water was a strong environmental predictor of leaf trait variation in response to seasonal variation. Reduced soil water availability during the dry season was associated with increased leaf thickness and water mass per area, possibly as a result of stomatal closure. Our findings advocate the need to account for environmental seasonality when studying leaf traits in seasonal ecosystems such as tropical forests.

The Syngameon Enigma

Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.

Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation

The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.