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Urbina, I.; Grau, O.; Sardans, J.; Ninot, J.M.; Peñuelas, J. |
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Title |
Encroachment of shrubs into subalpine grasslands in the Pyrenees changes the plant-soil stoichiometry spectrum |
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Journal Article |
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Year |
2020 |
Publication |
Plant and Soil |
Abbreviated Journal |
Plant Soil |
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448 |
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1-2 |
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37-53 |
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Nutrient stocks; Plant strategy; Plant-soil stoichiometry; Shrub encroachment; Subalpine grassland succession; aboveground biomass; biogeochemical cycle; carbon sequestration; ectomycorrhiza; fungus; grass; nitrogen; nutrient uptake; shrub; soil-vegetation interaction; stoichiometry; subalpine environment; succession; Europe; Pyrenees; Fungi |
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Aims: Shrub encroachment has been reported over a large proportion of the subalpine grasslands across Europe and is expected to have an important impact on the biogeochemical cycle of these ecosystems. We investigated the stoichiometric changes in the plant-soil system along the succession (e.g. increase in encroachment from unencroached grassland to mature shrubland) at two contrasting sites in the Pyrenees. Methods: We analyzed the chemical composition (C, N,15N, P, K, Ca, Mg and Fe) in the soil and in the aboveground plant compartments (leaves, leaf-litter and stems) of the main herbaceous species and shrubs at three contrasting stages of the succession: unencroached grassland, young shrubland and mature shrubland. Results: The plant-soil stoichiometry spectrum differed between the successional stages. Shrub encroachment generally increased the concentration of C and Ca and the C:N ratio and often reduced to concentrations of N, P and K in the leaves and leaf-litter, while several soil nutrient concentrations (N, P, K Ca and Mg) decreased. The stocks of C, N, P, Ca, and Mg in the total aboveground biomass increased with encroachment. Conclusions: Shrub encroachment favored the dominance of long-lived species with low concentrations of N and P in the plant-soil compartments, high C:nutrient ratios in the aboveground biomass and increase the uptake of N through ericoid or ectomycorrhizal fungi. We highlight the role of shrubs in the sequestration of C and nutrients through the allocation to the aboveground biomass. The changes in plant-soil elemental composition and stocks suggest a slowdown of the biogeochemical cycles in the subalpine mountain areas where shrub encroachment occurred. © 2020, Springer Nature Switzerland AG. |
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Biodiversity Research Institute (IRBio) and Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Catalonia, Spain |
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0032079x (Issn) |
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EcoFoG @ webmaster @ |
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983 |
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Sebbenn, A.M.; Blanc-Jolivet, C.; Mader, M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Honorio Coronado, E.N.; García-Dávila, C.; Tysklind, N.; Troispoux, V.; Delcamp, A.; Degen, B. |
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Title |
Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia |
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Journal Article |
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Year |
2019 |
Publication |
Conservation Genetics Resources |
Abbreviated Journal |
Conserv. Gen. Res. |
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11 |
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3 |
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341-343 |
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DNA fingerprints; Geographical origin; Jacaranda copaia; MassARRAY; MiSeq; RADSeq; Tropical timber |
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Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin. |
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BIOGECO, INRA, Univ. Bordeaux, Cestas, 33610, France |
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Springer Netherlands |
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18777252 (Issn) |
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EcoFoG @ webmaster @ |
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907 |
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Tysklind, N.; Blanc-Jolivet, C.; Mader, M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Honorio Coronado, E.N.; García-Dávila, C.R.; Sebbenn, A.M.; Caron, H.; Troispoux, V.; Guichoux, E.; Degen, B. |
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Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species |
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Journal Article |
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2019 |
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Conservation Genetics Resources |
Abbreviated Journal |
Conserv. Gen. Res. |
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11 |
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3 |
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337-339 |
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Carapa guianensis; Carapa surinamensis; DNA-fingerprints; Geographical origin; MassARRAY; MiSeq; RADSeq; Tropical timber |
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Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping. |
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BIOGECO, INRA, University Bordeaux, Cestas, 33610, France |
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Springer Netherlands |
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18777252 (Issn) |
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EcoFoG @ webmaster @ |
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909 |
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Brousseau, L.; Tinaut, A.; Duret, C.; Lang, T.; Garnier-Gere, P.; Scotti, I. |
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Title |
High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species |
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Journal Article |
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Year |
2014 |
Publication |
BMC Genomics |
Abbreviated Journal |
BMC Genomics |
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15 |
Issue |
238 |
Pages |
1-13 |
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454-Pyrosequencing; Polymorphism discovery; Tropical rainforest tree species |
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Background: 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. Results: In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.Conclusion: The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species. © 2014 Brousseau et al.; licensee BioMed Central Ltd. |
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BIOGECO, UMR 1202, University of Bordeaux, F-33400 Talence, France |
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BioMed Central Ltd. |
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14712164 (Issn) |
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Export Date: 18 April 2014; Source: Scopus; Art. No.: 238; Coden: Bgmee; Language of Original Document: English; Correspondence Address: Scotti, I.; INRA, UMR 0745 EcoFoG, Campus agronomique BP 709, F-97387 Cedex, France; email: ivan.scotti@ecofog.gf |
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537 |
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Mouillot, D.; Bellwood, D.R.; Baraloto, C.; Chave, J.; Galzin, R.; Harmelin-Vivien, M.; Kulbicki, M.; Lavergne, S.; Lavorel, S.; Mouquet, N.; Paine, C.E.T.; Renaud, J.; Thuiller, W. |
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Title |
Rare Species Support Vulnerable Functions in High-Diversity Ecosystems |
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Journal Article |
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2013 |
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PLoS Biology |
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PloS Biol. |
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11 |
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5 |
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e1001569 |
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Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning. © 2013 Mouillot et al. |
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Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom |
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15449173 (Issn) |
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Export Date: 12 June 2013; Source: Scopus; Art. No.: e1001569; Coden: Pblib; :doi 10.1371/journal.pbio.1001569; Language of Original Document: English; Correspondence Address: Mouillot, D.; Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS)-UM2, Institut français de recherche pour l'exploitation de la mer (IFREMER), Institute for Research and Development (IRD) 5119 ECOSYM, Université Montpellier 2 cc 093, Montpellier, France; email: david.mouillot@univ-montp2.fr |
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EcoFoG @ webmaster @ |
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492 |
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Duplais, C.; Papon, N.; Courdavault, V. |
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Title |
Tracking the Origin and Evolution of Plant Metabolites |
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Journal Article |
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2020 |
Publication |
Trends in Plant Science |
Abbreviated Journal |
Trends Plant Sci. |
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25 |
Issue |
12 |
Pages |
1182-1184 |
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enzyme evolution; iridoids; Lamiaceae; nepetalactone; plant metabolites |
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Iridoids are monoterpenes that are produced by various plants as chemical defense molecules. Lichman et al. recently described the timeline of molecular events that underpin the re-emergence of iridoid biosynthesis in an independent lineage of aromatic plants (catnip). This study represents a benchmark for studying enzyme and metabolite evolution in different clades across the tree of life. © 2020 Elsevier Ltd |
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Biomolécules et Biotechnologies Végétales (BBV) EA 2106, Université de Tours, Tours, France |
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Elsevier Ltd |
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13601385 (Issn) |
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EcoFoG @ webmaster @ |
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937 |
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Trzcinski, M.K.; Srivastava, D.S.; Corbara, B.; Dezerald, O.; Leroy, C.; Carrias, J.-F.; Dejean, A.; Céréghino, R.; Rudolf, V. |
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The effects of food web structure on ecosystem function exceeds those of precipitation |
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Journal Article |
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2016 |
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Journal of Animal Ecology |
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Journal of Animal Ecology |
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85 |
Issue |
5 |
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1147-1160 |
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bromeliad; climate change; community interactions; drought; ecosystem function; French Guiana; invertebrates; micro-organisms; phytotelmata; precipitation |
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Ecosystems are being stressed by climate change, but few studies have tested food web responses to changes in precipitation patterns and the consequences to ecosystem function. Fewer still have considered whether results from one geographic region can be applied to other regions, given the degree of community change over large biogeographic gradients. We assembled, in one field site, three types of macroinvertebrate communities within water-filled bromeliads. Two represented food webs containing both a fast filter feeder–microbial and slow detritivore energy channels found in Costa Rica and Puerto Rico, and one represented the structurally simpler food webs in French Guiana, which only contained the fast filter feeder–microbial channel. We manipulated the amount and distribution of rain entering bromeliads and examined how food web structure mediated ecosystem responses to changes in the quantity and temporal distribution of precipitation. Food web structure affected the survival of functional groups in general and ecosystem functions such as decomposition and the production of fine particulate organic matter. Ecosystem processes were more affected by decreased precipitation than were the abundance of micro-organisms and metazoans. In our experiments, the sensitivity of the ecosystem to precipitation change was primarily revealed in the food web dominated by the single filter feeder–microbial channel because other top-down and bottom-up processes were weak or absent. Our results show stronger effects of food web structure than precipitation change per se on the functioning of bromeliad ecosystems. Consequently, we predict that ecosystem function in bromeliads throughout the Americas will be more sensitive to changes in the distribution of species, rather than to the direct effects caused by changes in precipitation. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society |
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Boulevard de la Lironde, IRD, botAnique et bioinforMatique de l'Architecture des Plantes (UMR-IRD 123), TA A-51/PS2, Montpellier Cedex 5, France |
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Export Date: 1 September 2016 |
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EcoFoG @ webmaster @ |
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685 |
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Fayad, I.; Baghdadi, N.; Bailly, J.-S.; Barbier, N.; Gond, V.; Herault, B.; El Hajj, M.; Fabre, F.; Perrin, J. |
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Regional scale rain-forest height mapping using regression-kriging of spaceborne and airborne LiDAR data: Application on French Guiana |
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Journal Article |
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2016 |
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Remote Sensing |
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Remote Sensing |
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8 |
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3 |
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240 |
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Airborne LiDAR; Canopy height mapping; Forests; French Guiana; ICESat GLAS |
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LiDAR data has been successfully used to estimate forest parameters such as canopy heights and biomass. Major limitation of LiDAR systems (airborne and spaceborne) arises from their limited spatial coverage. In this study, we present a technique for canopy height mapping using airborne and spaceborne LiDAR data (from the Geoscience Laser Altimeter System (GLAS)). First, canopy heights extracted from both airborne and spaceborne LiDAR were extrapolated from available environmental data. The estimated canopy height maps using Random Forest (RF) regression from airborne or GLAS calibration datasets showed similar precisions (~6 m). To improve the precision of canopy height estimates, regression-kriging was used. Results indicated an improvement in terms of root mean square error (RMSE, from 6.5 to 4.2 m) using the GLAS dataset, and from 5.8 to 1.8 m using the airborne LiDAR dataset. Finally, in order to investigate the impact of the spatial sampling of future LiDAR missions on canopy height estimates precision, six subsets were derived from the initial airborne LiDAR dataset. Results indicated that using the regression-kriging approach a precision of 1.8 m on the canopy height map was achievable with a flight line spacing of 5 km. This precision decreased to 4.8 m for flight line spacing of 50 km. © 2016 by the authors. |
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BRGM, 3 Avenue Claude Guillemin, Orléans, France |
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Export Date: 22 April 2016 |
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EcoFoG @ webmaster @ |
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675 |
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Young, E.F.; Belchier, M.; Hauser, L.; Horsburgh, G.J.; Meredith, M.P.; Murphy, E.J.; Pascoal, S.; Rock, J.; Tysklind, N.; Carvalho, G.R. |
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Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species |
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2015 |
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Evolutionary Applications |
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Evolutionary Applications |
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8 |
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5 |
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486-509 |
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Notothenia rossii; Champsocephalus gunnari; Connectivity; Individual-based Modelling; Ocean circulation; Planktonic dispersal; Population genetics; Scotia Sea |
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Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts. © 2015 The Authors. |
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Campus Agronomique, Kourou Cedex, France |
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Export Date: 28 May 2015 |
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604 |
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Garcia-Davila, C.; Aldana Gomero, D.; Renno, J.-F.; Diaz Soria, R.; Hidalgo Pizango, G.; Flores Llampazo, G.; Castro-Ruiz, D.; Mejia de Loayza, E.; Angulo Chavez, C.; Mader, M.; Tysklind, N.; Paredes-Villanueva, K.; del Castillo Torres, D.; Degen, B.; Honorio Coronado, E.N. |
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Molecular evidence for three genetic species of Dipteryx in the Peruvian Amazon |
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Journal Article |
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2020 |
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Genetica |
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Genetica |
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148 |
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1 |
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1-11 |
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D. micrantha; Dipteryx charapilla; Genetic diversity; Microsatellites; Sequencing; Shihuahuaco; microsatellite DNA; plant DNA; allele; Dipteryx; DNA sequence; genetic variation; genetics; genotype; haplotype; Peru; phylogeny; plastid; river; species difference; Alleles; Dipteryx; DNA, Plant; Genetic Variation; Genotype; Haplotypes; Microsatellite Repeats; Peru; Phylogeny; Plastids; Rivers; Sequence Analysis, DNA; Species Specificity |
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Abstract |
There is a high international demand for timber from the genus Dipteryx, or “shihuahuaco” as it is known in Peru. Developing tools that allow the identification and discrimination of Dipteryx species is therefore important for supporting management of natural populations and to underpin legal trade of its timber. The objective of this study was the molecular characterization of Dipteryx species in the Peruvian Amazonia. Two plastid regions (cpDNA: trnH–psbA and matK) were sequenced and 11 microsatellite markers (nDNA) were genotyped for 32 individuals identified as Dipteryx charapilla, D. micrantha morphotype 1 and D. micrantha morphotype 2. Using the concatenated sequences of the plastid genes, we identified ten haplotypes that were not shared between the species or between the D. micrantha morphotypes. Haplotypic diversity was greater in D. micrantha morphotype 2 and D. charapilla than in D. micrantha morphotype 1, which presented only one haplotype with a wide distribution in Peru. The microsatellites allowed the discrimination of the same three clades and identified diagnostic alleles for each clade. These results allowed us to demonstrate that the two morphotypes of D. micrantha are different at both the plastid and nuclear markers, which supports the existence of three genetically distinct species in Peru. This study provides information for the genetic discrimination of Dipteryx species and emphasises the importance of conserving the genetic variability of this genus in the Peruvian Amazonia. © 2019, Springer Nature Switzerland AG. |
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Carrera de Ingeniería Foresta, Laboratorio de Dendrocronología, Facultad de Ciencias Agrícolas, Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito, Santa Cruz, Bolivia |
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Springer |
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00166707 (Issn) |
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EcoFoG @ webmaster @ |
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990 |
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