Causes and consequences of large clonal assemblies in a poplar hybrid zone

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this study, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with Populus tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional genotyping-by-sequencing data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed from P. tremula, which may have favoured their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically extended individuals does not threaten population survival

Geography determines genetic relationships between species of mountain pine (Pinus mugo complex) in western Europe

Aim  Our aims were to test whether morphological species of mountain pines were genetically supported in the western part of the distribution range of the Pinus mugo species complex (Pinus mugo Turra sensu lato), to resolve genetically homogeneous clusters of populations, to determine historical demographic processes, and to assess the potential hybridization of mountain pines with Scots pine, Pinus sylvestris L. Location  Populations were sampled in the Iberian System, the Pyrenees, the French Mont Ventoux, Vosges and Jura mountains, the German Black Forest and throughout the Alps. This corresponded to a range-wide sampling for mountain pine sensu stricto (Pinus uncinata Ram.) and to a sampling of the western parts of the ranges of dwarf mountain pine (Pinus mugo Turra sensu stricto) and bog pine/peatbog pine [Pinus rotundata Link/Pinus × pseudopumilio (Willk.) Beck]. Methods  In total, 786 individuals of P. mugo sensu lato from 29 natural populations, and 85 individuals of P. sylvestris from four natural populations were genotyped at three chloroplast microsatellites (cpSSRs). Populations were characterized for standard genetic diversity statistics and signs of demographic expansion. Genetic structure was explored using analysis of molecular variance, differentiation statistics and Bayesian analysis of population structure (BAPS). Results  One hundred haplotypes were identified in P. mugo sensu lato. There was a stronger differentiation between geographical regions than between morphologically identified taxa (P. mugo sensu stricto, P. uncinata and P. rotundata/P. ×pseudopumilio). Overall genetic differentiation was weak (GST = 0.070) and displayed a clear phylogeographic structure [NST = 0.263, NST > NST (permuted), P < 0.001]. BAPS identified a Pyrenean and an Alpine gene pool, along with several smaller genetic clusters corresponding to peripheral populations. Main conclusions  The core regions of the Pyrenees and Alps were probably recolonized, respectively by P. uncinata and P. uncinata/P. mugo sensu stricto, from multiple glacial refugia that were well connected by pollen flow within the mountain chains. Pinus rotundata/P. × pseudopumilio populations from the Black Forest, Vosges and Jura mountains were probably recolonized from various glacial populations that kept their genetic distinctiveness despite late glacial and early Holocene expansion. Marginal P. uncinata populations from the Iberian System are compatible with elevational shifts and long-term isolation. The causes of haplotype sharing between P. mugo sensu lato and P. sylvestris require further researc

Divergent selection in a Mediterranean pine on local spatial scales

1. The effects of selection on an organism's genome are hard to detect on small spatial scales, as gene flow can swamp signatures of local adaptation. Therefore, most genome scans to detect signatures of environmental selection are performed on large spatial scales; however, divergent selection on the local scale (e.g. between contrasting soil conditions) has also been demonstrated, in particular for herbaceous plants. 2. Here, we hypothesised that in topographically complex landscapes, microenvironment variability is strong enough to leave a selective footprint in the genomes of long-lived organisms. To test this, we investigated paired south- versus north-facing Pinus pinaster stands on the local scale, with trees growing in close vicinity (≤820 m distance between paired south- and north-facing stands), in a Mediterranean mountain area. While trees on north-facing slopes experience less radiation, trees on south-facing slopes suffer from especially harsh conditions, particularly during the dry summer season. 3. Two outlier analyses consistently revealed five putatively adaptive loci (out of 4034), in candidate genes two of which encoded non-synonymous substitutions. Additionally, one locus showed consistent allele frequency differences in all three stand pairs indicating divergent selection despite high gene flow on the local scale. Permutation tests demonstrated that our findings were robust. 4. Functional annotation of these candidate genes revealed biological functions related to abiotic stress response, such as water availability, in other plant species. 5. Synthesis. Our study highlights how divergent selection in heterogeneous microenvironments shapes and maintains the functional genetic variation within populations of long-lived forest tree species, being the first to focus on adaptive genetic divergence between south- and north-facing slopes within continuous forest stands. This is especially relevant in the current context of climate change, as this variation is at the base of plant population responses to future climate.European Commission http://dx.doi.org/10.13039/501100000780European Science Foundation http://dx.doi.org/10.13039/501100000782Spanish Ministry of Science and Innovation http://dx.doi.org/10.13039/501100004837University of BrodeauxPeer Reviewe

Biogeography and evolution of seeder and resprouter forms of Erica coccinea (Ericaceae) in the fire-prone Cape fynbos

The genus Erica represents the epitome of plant biodiversity in the South African Cape fynbos with over 700 species. This genus is composed of seeder and resprouter species, but both species diversity and endemism are strongly linked to the seeder habit and concentrated in the southwestern Cape Floristic Region (CFR). Erica coccinea is a relatively abundant and widespread fynbos species whose most remarkable morphological feature is the existence of distinct seeder and resprouter forms, frequently—but not always—in disjunct populations. Both higher within- population genetic diversity and among-population differentiation have been found in seeders, most likely as a consequence of the shorter generation times and faster population turnovers. Resprouters, despite being less diverse, are suspected to be ancestral. However, no solid evidence has yet been provided for the ancestrality of the resprouter form, or for the demographic processes that have determined the current distribution of genetic diversity in both regeneration forms. Here, we used microsatellites and sequences of the nuclear ribosomal internal transcribed spacers to describe the phylogeographic structure of seeder and resprouter E. c occinea populations and provide good evidence for the ancestral status of the resprouter form and the comparatively high rates of molecular evolution in derived seeder populations. We also reveal that mixed populations, where both seeder and resprouter individuals co-occur, were originated by secondary contacts. This study highlights the role of fire in driving accelerated diversification in seeder lineages of highly speciose CFR fynbos taxa

The hyperdominant tropical tree <i>Eschweilera coriacea</i> (Lecythidaceae) shows higher genetic heterogeneity than sympatric Eschweilera species in French Guiana

International audienceBackground and aims – The evolutionary history of Amazonia’s hyperabundant tropical tree species, also known as “hyperdominant” species, remains poorly investigated. We assessed whether the hyperdominant Eschweilera coriacea (DC.) S.A.Mori (Lecythidaceae) represents a single genetically cohesive species, and how its genetic constitution relates to other species from the same clade with which it occurs sympatrically in French Guiana.Methods – We sampled 152 individuals in nine forest sites in French Guiana, representing 11 species of the genus Eschweilera all belonging to the Parvifolia clade, with emphasis on E. coriacea. Samples were genotyped at four simple sequence repeat (SSR) markers. We delimited gene pools, i.e., genetically coherent putative taxa, using STRUCTURE software and principal component analysis. We compared the genetic assignment of individuals with their morphological species determination and estimated genetic diversity and differentiation for gene pools and species. We also estimated genome size using flow cytometry.Key results – SSR profiles commonly displayed up to four alleles per genotype, suggesting that the investigated Eschweilera species bear a paleopolyploid signature. Flow cytometry suggested that the studied species are diploid with haploid genome sizes of 871–1046 Mbp. We detected five gene pools and observed a good correspondence between morphological and genetic delimitation for Eschweilera sagotiana Miers and the undescribed morphospecies E. sp. 3 (which resembles E. grandiflora (Aubl.) Sandwith), and to a lesser extent for E. decolorans Sandwith and E. micrantha (O.Berg) Miers. Eschweilera coriacea was the most genetically diverse species and included individuals assigned to each gene pool.Conclusions – We found no conclusive evidence for cryptic species within E. coriacea in French Guiana. SSRs detected fewer gene pools than expected based on morphology in the Parvifolia clade but discriminated evolutionary relationships better than available plastid markers. A positive trend between demographic abundance of species and allelic richness illustrates that hyperdominants may have a high evolutionary potential. This hypothesis can be tested using more powerful genomic data in combination with tree phenotypic trait variation and characterization of niche breadth, to enhance our understanding of the causes of hyperdominance in Amazonian trees

Ancient and historical DNA in conservation policy

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (N-e), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.Peer reviewe

Guideline Materials and Documentation for the Genetic Diversity Indicators of the Monitoring Framework for the Kunming-Montreal Global Biodiversity Framework

Genetic diversity is fundamental to biological diversity, vital for species’ health and adaptation to environmental change. Under the recently adopted Kunming-Montreal Global Biodiversity Framework (GBF), 196 Parties committed to report the status of genetic diversity for both wild and domesticated species. For this, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: ensuring that populations are large enough to maintain genetic diversity (effective population size Ne 500 indicator) and maintaining genetically distinct populations (populations maintained, PM indicator). A third indicator focuses on the number of species being monitored using DNA-based methods. Adopted by 196 CBD Parties in December 2022, GBF integrated Ne 500 and PM as headline and complementary indicators, respectively. To aid nations in quantifying these indicators, a detailed set of guideline materials was developed, encompassing species selection, data compilation, and indicator computation. These guidelines draw from the collaborative efforts of the first multinational assessment of genetic diversity indicators that was recently completed and that will be refined continually through a versioning system, as more experience is gained and shared. The materials aim to support the global monitoring framework established by the CBD and are accessible online for utilization and updates. The guidelines are available at this link.