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

Stepping stones to isolation: impacts of a changing climate on the connectivity of fragmented fish populations

In the marine environment, understanding the biophysical mechanisms that drive variability in larval dispersal and population connectivity is essential for estimating the potential impacts of climate change on the resilience and genetic structure of populations. Species whose populations are small, isolated, and discontinuous in distribution will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant, and frequently exchange conspecifics. Here, we use an Individual Based Modelling approach, combined with a population genetics projection model, to consider the impacts of a warming climate on the population connectivity of two contrasting Antarctic fish species, Notothenia rossii and Champsocephalus gunnari. Focussing on the Scotia Sea region, sea surface temperatures are predicted to increase significantly by the end of the 21st century, resulting in reduced planktonic duration and increased egg and larval mortality. With shorter planktonic durations, the results of our study predict reduced dispersal of both species across the Scotia Sea, from Antarctic Peninsula sites to islands in the north and east, and increased dispersal among neighbouring sites, such as around the Antarctic Peninsula. Increased mortality modified the magnitude of population connectivity but had little effect on the overall patterns. Whilst the predicted changes in connectivity had little impact on the projected regional population genetic structure of N. rossii, which remained broadly genetically homogeneous within distances of ~1500 km, the genetic isolation of C. gunnari populations in the northern Scotia Sea was predicted to increase with rising sea temperatures. Our study highlights the potential for increased isolation of island populations in a warming world, with implications for the resilience of populations and their ability to adapt to ongoing environmental change, a matter of high relevance to fisheries and ecosystem-level management

Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical tree

1. Trait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unknown. Moreover, we do not know how consistent is the response between organ vs. whole-tree level. 2. We examined phenotypic variability for 16 functional leaf (dimensions, nutrient, chlorophyll) and wood traits (density) across two soil types, Ferralitic Soil (FS) vs. White Sands (WS), on two sites for 70 adult trees of Cecropia obtusa Trécul (Urticaceae) in French Guiana. Cecropia is a widespread pioneer Neotropical genus that generally dominates early successional forest stages. To understand how soil types impact resource use through the processes of growth and branching, we examined the architectural development with a retrospective analysis of growth trajectories. We expect soil types to affect both, functional traits in relation to resource acquisition strategy as already described at the interspecific level, and growth strategies due to resource limitations with reduced growth on poor soils. 3. Functional traits were not involved in the soil response, as only two traits -leaf residual water content and K content-showed significant differences across soil types. Soil effects were stronger on growth trajectories, with WS trees having the slowest growth trajectories and less numerous branches across their lifespan. 4. The analysis of growth trajectories based on architectural analysis improved our ability to characterise the response of trees with soil types. The intraspecific variability is higher for growth trajectories than functional traits for  C. obtusa, revealing the complementarity of the architectural approach with the functional approach to gain insights on the way trees manage their resources over their lifetime. Soil-related responses of Cecropia functional traits are not the same as those at the interspecific level, suggesting that the effects of the acting ecological processes are different between the two levels. Apart from soil differences, much variation was found across sites, which calls for further investigation of the factors shaping growth trajectories in tropical forests

Timber tracking of Jacaranda copaia from the Amazon forest using DNA fingerprinting

We investigated the utility of nuclear and cytoplasmic single nucleotide polymorphism (SNP) markers for timber tracking of the intensively logged and commercialized Amazonian tree Jacaranda copaia. Eight hundred and thirty-two trees were sampled (cambium or leaves) from 38 sampling sites in Bolivia, Brazil, French Guiana, and Peru. A total of 128 SNP markers (113 nuclear, 11 chloroplastic, and 4 mitochondrial) were used for genotyping the samples. Bayesian cluster analyses were carried out to group individuals into homogeneous genetic groups for tests to self-assign groups of individuals or individuals to their population of origin. Cluster analysis based on all the SNP markers detected seven main genetic groups. Genetic differentiation was high among populations (0.484) and among genetic groups (0.415), and populations showed a strong isolation-by-distance pattern. Self-assignment testing of the groups of individuals for all loci was able to determine the population origin of all the samples (accuracy = 100%). Self-assignment tests of individuals were able to assign the origin of 94.5%–100% of individuals (accuracy: 91.7%–100%). Our results show that the use of the 128 SNP markers is suitable to correctly determine the origin of J. copaia timber, and they should be considered a useful tool for customs and local and international police

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Marqueurs génétiques des populations dans les programmes de biosurveillance : Une étude de cas sur les poissons plats dans les îles britanniques

The use of bioindicator fish species in monitoring programmes is widely accepted as a means of assessing marine environmental health. In such approaches, the effects of pollutants and other anthropogenic impacts on the health of individual fish is evaluated and compared to that of non-exposed reference fish. However, not all fish are the same. Genetic diversity between individuals translates into variance on how and when individuals respond to pollution, and the combined response of interbreeding individuals is reflected on how a population is affected by exposure to environmental stressors such as pollutants.Whether due to natural causes or the result of previous pollution exposure and selection, some populations may be more tolerant to pollutant exposure than others. If not corrected, comparisons of disease profiles among populations with differing pollution tolerance levels will affect the interpretation of results from biomonitoring programmes.In the UK, dab, Limanda limanda, and flounder, Platichthys flesus, are routinely used as environmental bioindicators of pollutant exposure; however, little information exists on population structuring among sampling locations. Here, the development of neutral microsatellite markers for dab and flounder is described. A novel approach for reducing the cost of labelling microsatellite primers in combination with multiple amplification of several loci in a single tube is then devised. Next, the development and preliminary evaluation of adaptive genetic markers to detect selection imposed by pollution is reported. No definitive evidence of strong and recent selective pressures at the analyzed genes is found, but suggestions for future research are made. Estimating genetic differentiation between populations is central in population genetic studies. Several new and traditional estimators of genetic differentiation are compared empirically. Consecutively, the genetic structure of dab around the British Isles is analysed and described. Two main dab subpopulations, subtly but significantly differentiated, have been identified, corresponding to the North Sea and Irish Sea basins, though there is also evidence of structuring at other scales. The implications for biomonitoring programmes are considered. Finally the combination of both genetic and biomonitoring information is explored. No evidence of increased relatedness or inbreeding among individuals afflicted with liver nodules is found, however, for some samples with abnormally high frequency of liver nodules, the incidence can be explained by recent immigration from other locations. Genotyping of assessed individuals provided important information not available by other means and the incorporation of population genetic data is encouraged for biomonitoring programmes studying mobile species.L'utilisation d'espèces de poissons bioindicateurs dans les programmes de surveillance est largement acceptée comme un moyen d'évaluer la santé du milieu marin. Dans ces approches, les effets des polluants et autres impacts anthropogéniques sur la santé de chaque poisson sont évalués et comparés à ceux de poissons de référence non exposés. Cependant, tous les poissons ne sont pas identiques. La diversité génétique entre les individus se traduit par une variance dans la manière et le moment où les individus répondent à la pollution, et la réponse combinée des individus qui se croisent se reflète dans la manière dont une population est affectée par l'exposition à des facteurs de stress environnementaux tels que les polluants.Que cela soit dû à des causes naturelles ou au résultat d'une exposition antérieure à la pollution et d'une sélection, certaines populations peuvent être plus tolérantes à l'exposition aux polluants que d'autres. Si elles ne sont pas corrigées, les comparaisons des profils de maladies entre des populations ayant des niveaux de tolérance à la pollution différents affecteront l'interprétation des résultats des programmes de biosurveillance.Au Royaume-Uni, la limande, Limanda limanda, et le flet, Platichthys flesus, sont couramment utilisés comme bioindicateurs environnementaux de l'exposition aux polluants ; cependant, il existe peu d'informations sur la structuration des populations entre les sites d'échantillonnage. Nous décrivons ici le développement de marqueurs microsatellites neutres pour la limande et le flet. Une nouvelle approche pour réduire le coût du marquage des amorces microsatellites en combinaison avec l'amplification multiple de plusieurs loci dans un seul tube est ensuite conçue. Ensuite, le développement et l'évaluation préliminaire de marqueurs génétiques adaptatifs pour détecter la sélection imposée par la pollution sont rapportés. Aucune preuve définitive de pressions sélectives fortes et récentes au niveau des gènes analysés n'est trouvée, mais des suggestions de recherches futures sont faites. L'estimation de la différenciation génétique entre les populations est centrale dans les études de génétique des populations. Plusieurs estimateurs nouveaux et traditionnels de la différenciation génétique sont comparés empiriquement. Consécutivement, la structure génétique de la limande autour des îles britanniques est analysée et décrite. Deux sous-populations principales de limande, subtilement mais significativement différenciées, ont été identifiées, correspondant aux bassins de la mer du Nord et de la mer d'Irlande, bien qu'il y ait également des preuves de structuration à d'autres échelles. Les implications pour les programmes de biosurveillance sont examinées. Enfin, la combinaison des informations génétiques et de biosurveillance est explorée. Aucune preuve d'une parenté ou d'une consanguinité accrue parmi les individus atteints de nodules hépatiques n'est trouvée, cependant, pour certains échantillons présentant une fréquence anormalement élevée de nodules hépatiques, l'incidence peut être expliquée par une immigration récente en provenance d'autres endroits. Le génotypage des individus évalués a fourni des informations importantes non disponibles par d'autres moyens et l'incorporation de données génétiques de population est encouragée pour les programmes de biosurveillance étudiant des espèces mobiles

Population genetic markers in biomonitoring programmes : A case study of flatfish around the British Isles

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