German Federal Ministry of Food and Agriculture ; Conseil Regional d'Aquitaine ; European Union ; FEDER ; Investissements d'avenir ; Conseil Regional d'Aquitaine: 20030304002FA ; Conseil Regional d'Aquitaine: 20040305003FA ; FEDER: 2003227 ; Investissements d'avenir: ANR-10-EQPX-16-01 ; Investissements d'avenir: CEBA: ANR-10-LABX-25-01 ; : 001-2016-SERFOR-DGGSPFFS-DGSPF ; 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.
German Federal Ministry of Food and Agriculture (BMEL) ; Programa Nacional de Innovacion para la Competitividad y Productividad ; Conseil Regional d'Aquitaine ; European Union, FEDER ; Programa Nacional de Innovacion para la Competitividad y Productividad: 381-PNICP-PIAP-2014 ; Conseil Regional d'Aquitaine: 20030304002FA ; Conseil Regional d'Aquitaine: 20040305003FA ; European Union, FEDER: 2003227 ; European Union, FEDER: ANR-10-EQPX-16-01 ; European Union, FEDER: ANR-10-LABX-25-01 ; We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia.
German Federal Ministry of Food and Agriculture (BMEL) ; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) ; Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest ; European Union, FEDER ; Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest: ANR-10-EQPX-16-01 ; European Union, FEDER: ANR-10-EQPX-16-01 ; European Union, FEDER: 2003227 ; European Union, FEDER: ANR-10-LABX-25-01 ; We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed.
Aim: The accurate mapping of forest carbon stocks is essential for understanding the global carbon cycle, for assessing emissions from deforestation, and for rational land-use planning. Remote sensing (RS) is currently the key tool for this purpose, but RS does not estimate vegetation biomass directly, and thus may miss significant spatial variations in forest structure. We test the stated accuracy of pantropical carbon maps using a large independent field dataset. Location: Tropical forests of the Amazon basin. The permanent archive of the field plot data can be accessed at: http://dx.doi.org/10.5521/FORESTPLOTS.NET/2014_1 Methods: Two recent pantropical RS maps of vegetation carbon are compared to a unique ground-plot dataset, involving tree measurements in 413 large inventory plots located in nine countries. The RS maps were compared directly to field plots, and kriging of the field data was used to allow area-based comparisons. Results: The two RS carbon maps fail to capture the main gradient in Amazon forest carbon detected using 413 ground plots, from the densely wooded tall forests of the north-east, to the light-wooded, shorter forests of the south-west. The differences between plots and RS maps far exceed the uncertainties given in these studies, with whole regions over- or under-estimated by > 25%, whereas regional uncertainties for the maps were reported to be < 5%. Main conclusions: Pantropical biomass maps are widely used by governments and by projects aiming to reduce deforestation using carbon offsets, but may have significant regional biases. Carbon-mapping techniques must be revised to account for the known ecological variation in tree wood density and allometry to create maps suitable for carbon accounting. The use of single relationships between tree canopy height and above-ground biomass inevitably yields large, spatially correlated errors. This presents a significant challenge to both the forest conservation and remote sensing communities, because neither wood density nor species ...
This paper is the result of the work of hundreds of different scientists and research institutions in the Amazon over the past 80 years. Without their hard work this analysis would have been impossible. We thank Charles Zartman for the use of plots from Jutai. HtS, VFG, and RS were supported by grant 407232/2013-3 - PVE - MEC/MCTI/CAPES/CNPq/FAPs; PIP had support for this work from CNPq (productivity grant 310885/2017-5) and FAPESP (research grant #09/53413-5); RAFL was supported by the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 795114; CB was supported by grant FAPESP 95/3058-0 - CRS 068/96 WWF Brasil - The Body Shop; DS, JFM, JE, PP and JC benefited from an "Investissement d'Avenir" grant managed by the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01); HLQ/MAP/JLLM received financial supported by MCT/CNPq/CT-INFRA/GEOMA #550373/2010-1 and # 457515/2012-0, and JLLM were supported by grant CAPES/PDSE # 88881.135761/2016-01 and CAPES/Fapespa #1530801; The Brazilian National Research Council (CNPq) provided a productivity grant to EMV (Grant 308040/2017-1); Floristic identification in plots in the RAINFOR forest monitoring network have been supported by the Natural Environment Research Council (grants NE/B503384/1, NE/ D01025X/1, NE/ I02982X/1, NE/F005806/1, NE/D005590/1 and NE/I028122/1) and the Gordon and Betty Moore Foundation; BMF is funded by FAPESP grant 2016/25086-3. BSM, BHMJ and OLP were supported by grants CNPq/CAPES/ FAPS/BC-Newton Fund #441244/2016-5 and FAPEMAT/0589267/2016; TWH was funded by National Science Foundation grant DEB-1556338.The 25-ha Long-Term Ecological Research Project of Amacayacu is a collaborative project of the Instituto Amazónico de Investigaciones Científicas Sinchi and the Universidad Nacional de Colombia Sede Medellín, in partnership with the Unidad de Manejo Especial de Parques Naturales Nacionales and the Center for Tropical Forest Science of the Smithsonian Tropical Research Institute (CTFS). The Amacayacu Forest Dynamics Plot is part of the Center for Tropical Forest Science, a global network of large-scale demographic tree plots. We acknowledge the Director and staff of the Amacayacu National Park for supporting and maintaining the project in this National Park. ; Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come. ; Publisher PDF ; Peer reviewed
