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Eva, H. D., Belward, A. S., De Miranda, E. E., Di Bella, C. M., Gond, V., Huber, O., et al. (2004). A land cover map of South America. Glob. Change Biol., 10(5), 731–744.
Abstract: A digital land cover map of South America has been produced using remotely sensed satellite data acquired between 1995 and the year 2000. The mapping scale is defined by the 1 km spatial resolution of the map grid-cell. In order to realize the product, different sources of satellite data were used, each source providing either a particular parameter of land cover characteristic required by the legend, or mapping a particular land cover class. The map legend is designed both to fit requirements for regional climate modelling and for studies on land cover change. The legend is also compatible with a wider, global, land cover mapping exercise, which seeks to characterize the world's land surface for the year 2000. As a first step, the humid forest domain has been validated using a sample of high-resolution satellite images. The map demonstrates both the major incursions of agriculture into the remaining forest domains and the extensive areas of agriculture, which now dominate South America's grasslands.
Keywords: Amazonia; ecosystems; land cover; mapping; South America; vegetation classes
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Baraloto, C., Rabaud, S., Molto, Q., Blanc, L., Fortunel, C., Herault, B., et al. (2011). Disentangling stand and environmental correlates of aboveground biomass in Amazonian forests. Glob. Change Biol., 17(8), 2677–2688.
Abstract: Tropical forests contain an important proportion of the carbon stored in terrestrial vegetation, but estimated aboveground biomass (AGB) in tropical forests varies two-fold, with little consensus on the relative importance of climate, soil and forest structure in explaining spatial patterns. Here, we present analyses from a plot network designed to examine differences among contrasting forest habitats (terra firme, seasonally flooded, and white-sand forests) that span the gradient of climate and soil conditions of the Amazon basin. We installed 0.5-ha plots in 74 sites representing the three lowland forest habitats in both Loreto, Peru and French Guiana, and we integrated data describing climate, soil physical and chemical characteristics and stand variables, including local measures of wood specific gravity (WSG). We use a hierarchical model to separate the contributions of stand variables from climate and soil variables in explaining spatial variation in AGB. AGB differed among both habitats and regions, varying from 78 Mg ha(-1) in white-sand forest in Peru to 605 Mg ha(-1) in terra firme clay forest of French Guiana. Stand variables including tree size and basal area, and to a lesser extent WSG, were strong predictors of spatial variation in AGB. In contrast, soil and climate variables explained little overall variation in AGB, though they did co-vary to a limited extent with stand parameters that explained AGB. Our results suggest that positive feedbacks in forest structure and turnover control AGB in Amazonian forests, with richer soils (Peruvian terra firme and all seasonally flooded habitats) supporting smaller trees with lower wood density and moderate soils (French Guianan terra firme) supporting many larger trees with high wood density. The weak direct relationships we observed between soil and climate variables and AGB suggest that the most appropriate approaches to landscape scale modeling of AGB in the Amazon would be based on remote sensing methods to map stand structure.
Keywords: carbon stocks; climate; flooded forest; forest structure; French Guiana; Peru; REDD; soil properties; tropical rainforest; white-sand forest; wood specific gravity
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Stahl, C., Fontaine, S., Klumpp, K., Picon-Cochard, C., Grise, M. M., Dezecache, C., et al. (2017). Continuous soil carbon storage of old permanent pastures in Amazonia. Glob Change Biol, 23(8), 3382–3392.
Abstract: Amazonian forests continuously accumulate carbon (C) in biomass and in soil, representing a carbon sink of 0.42–0.65 GtC yr−1. In recent decades, more than 15% of Amazonian forests have been converted into pastures, resulting in net C emissions (~200 tC ha−1) due to biomass burning and litter mineralization in the first years after deforestation. However, little is known about the capacity of tropical pastures to restore a C sink. Our study shows in French Amazonia that the C storage observed in native forest can be partly restored in old (≥24 year) tropical pastures managed with a low stocking rate (±1 LSU ha−1) and without the use of fire since their establishment. A unique combination of a large chronosequence study and eddy covariance measurements showed that pastures stored between −1.27 ± 0.37 and −5.31 ± 2.08 tC ha−1 yr−1 while the nearby native forest stored −3.31 ± 0.44 tC ha−1 yr−1. This carbon is mainly sequestered in the humus of deep soil layers (20–100 cm), whereas no C storage was observed in the 0- to 20-cm layer. C storage in C4 tropical pasture is associated with the installation and development of C3 species, which increase either the input of N to the ecosystem or the C:N ratio of soil organic matter. Efforts to curb deforestation remain an obvious priority to preserve forest C stocks and biodiversity. However, our results show that if sustainable management is applied in tropical pastures coming from deforestation (avoiding fires and overgrazing, using a grazing rotation plan and a mixture of C3 and C4 species), they can ensure a continuous C storage, thereby adding to the current C sink of Amazonian forests.
Keywords: carbon storage; CN coupling; deep soil; mixed-grass pasture; native forest
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De Weirdt, M., Verbeeck, H., Maignan, F., Peylin, P., Poulter, B., Bonal, D., et al. (2012). Seasonal leaf dynamics for tropical evergreen forests in a process-based global ecosystem model. Geoscientific Model Dev., 5(5), 1091–1108.
Abstract: The influence of seasonal phenology on canopy photosynthesis in tropical evergreen forests remains poorly understood, and its representation in global ecosystem models is highly simplified, typically with no seasonal variation of canopy leaf properties taken into account. Including seasonal variation in leaf age and photosynthetic capacity could improve the correspondence of global vegetation model outputs with the wet-dry season CO2 patterns measured at flux tower sites in these forests. We introduced a leaf litterfall dynamics scheme in the global terrestrial ecosystem model ORCHIDEE based on seasonal variations in net primary production (NPP), resulting in higher leaf turnover in periods of high productivity. The modifications in the leaf litterfall scheme induce seasonal variation in leaf age distribution and photosynthetic capacity. We evaluated the results of the modification against seasonal patterns of three long-term in-situ leaf litterfall datasets of evergreen tropical forests in Panama, French Guiana and Brazil. In addition, we evaluated the impact of the model improvements on simulated latent heat (LE) and gross primary productivity (GPP) fluxes for the flux tower sites Guyaflux (French Guiana) and TapajÃ3s (km 67, Brazil). The results show that the introduced seasonal leaf litterfall corresponds well with field inventory leaf litter data and times with its seasonality. Although the simulated litterfall improved substantially by the model modifications, the impact on the modelled fluxes remained limited. The seasonal pattern of GPP improved clearly for the Guyaflux site, but no significant improvement was obtained for the TapajÃ3s site. The seasonal pattern of the modelled latent heat fluxes was hardly changed and remained consistent with the observed fluxes. We conclude that we introduced a realistic and generic litterfall dynamics scheme, but that other processes need to be improved in the model to achieve better simulations of GPP seasonal patterns for tropical evergreen forests. © Author(s) 2012. CC Attribution 3.0 License.
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Longo, M., Knox, R. G., Levine, N. M., Swann, A. L. S., Medvigy, D. M., Dietze, M. C., et al. (2019). The biophysics, ecology, and biogeochemistry of functionally diverse, vertically and horizontally heterogeneous ecosystems: The Ecosystem Demography model, version 2.2-Part 2: Model evaluation for tropical South America. Geoscientific Model Dev., 12(10), 4347–4374.
Abstract: The Ecosystem Demography model version 2.2 (ED-2.2) is a terrestrial biosphere model that simulates the biophysical, ecological, and biogeochemical dynamics of vertically and horizontally heterogeneous terrestrial ecosystems. In a companion paper (Longo et al., 2019a), we described how the model solves the energy, water, and carbon cycles, and verified the high degree of conservation of these properties in long-term simulations that include long-term (multi-decadal) vegetation dynamics. Here, we present a detailed assessment of the model's ability to represent multiple processes associated with the biophysical and biogeochemical cycles in Amazon forests. We use multiple measurements from eddy covariance towers, forest inventory plots, and regional remote-sensing products to assess the model's ability to represent biophysical, physiological, and ecological processes at multiple timescales, ranging from subdaily to century long. The ED-2.2 model accurately describes the vertical distribution of light, water fluxes, and the storage of water, energy, and carbon in the canopy air space, the regional distribution of biomass in tropical South America, and the variability of biomass as a function of environmental drivers. In addition, ED-2.2 qualitatively captures several emergent properties of the ecosystem found in observations, specifically observed relationships between aboveground biomass, mortality rates, and wood density; however, the slopes of these relationships were not accurately captured. We also identified several limitations, including the model's tendency to overestimate the magnitude and seasonality of heterotrophic respiration and to overestimate growth rates in a nutrient-poor tropical site. The evaluation presented here highlights the potential of incorporating structural and functional heterogeneity within biomes in Earth system models (ESMs) and to realistically represent their impacts on energy, water, and carbon cycles. We also identify several priorities for further model development.
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Woolfit, M., Iturbe-Ormaetxe, I., Brownlie, J. C., Walker, T., Riegler, M., Seleznev, A., et al. (2013). Genomic evolution of the pathogenic Wolbachia strain, wMelPop. Genome Biolog. Evol., 5(11), 2189–2204.
Abstract: Most strains of the widespread endosymbiotic bacterium Wolbachia pipientis are benign or behave as reproductive parasites. The pathogenic strain wMelPop is a striking exception, however: it overreplicates in its insect hosts and causes severe life shortening. The mechanism of this pathogenesis is currently unknown. We have sequenced the genomes of three variants of wMelPop and of the closely related nonpathogenic strain wMelCS. We show that the genomes of wMelCS and wMelPop appear to be identical in the nonrepeat regions of the genome and differ detectably only by the triplication of a 19-kb region that is unlikely to be associated with life shortening, demonstrating that dramatic differences in the host phenotype caused by this endosymbiont may be the result of only minor genetic changes. We also compare the genomes of the original wMelPop strain from Drosophila melanogaster and two sequentialderivatives, wMelPop-CLA and wMelPop-PGYP. To develop wMelPop as a novel biocontrol agent, it was first transinfected into and passaged in mosquito cell lines for approximately 3.5 years, generating wMelPop-CLA. This cell line-passaged strain was then transinfected into Aedesaegypti mosquitoes, creating wMelPop-PGYP,which wassequenced after 4yearsin the insecthost. We observe a rapid burst of genomic changes during cell line passaging, but no further mutations were detected after transinfection into mosquitoes, indicating either that host preadaptation had occurred in cell lines, that cell lines are a more selectively permissive environment than animal hosts, or both. Our results provide valuable data on the rates of genomic and phenotypic change in Wolbachia associated with host shifts over short time scales. © The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Keywords: Endosymbiont; Evolution; Genomics; Wolbachia
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Yatabe, Y., Kane, N. C., Scotti-Saintagne, C., & Rieseberg, L. H. (2007). Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H-petiolaris. Genetics, 175(4), 1883–1893.
Abstract: Plant species may remain morphologically distinct despite gene exchange with congeners, yet little is known about the genomewide pattern of introgression among species. Here we analyze the effects of persistent gene flow on genomic differentiation between the sympatric sunflower species Helianthus annuus and H. petiolaris. While the species are strongly isolated in testcrosses, genetic distances at 108 microsatellite loci and 14 sequenced genes are highly variable and much lower (on average) than for more closely related but historically allopatric congeners. Our analyses failed to detect a positive association between levels of genetic differentiation and chromosomal rearrangements (as reported in a prior publication) or proximity to QTL for morphological differences or hybrid sterility. However, a significant increase in differentiation was observed for markers within 5 cM of chromosomal breakpoints. Together, these results suggest that islands of differentiation between these two species are small, except in areas of low recombination. Furthermore, only microsatellites associated with ESTs were identified as outlier loci in tests for selection, which might indicate that the ESTs themselves are the targets of selection rather than linked genes (or that coding regions are not randomly distributed). In general, these results indicate that even strong and genetically complex reproductive barriers cannot prevent widespread introgression.
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Scotti-Saintagne, C., Mariette, S., Porth, I., Goicoechea, P. G., Barreneche, T., Bodenes, K., et al. (2004). Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q petraea (Matt.) Liebl.]. Genetics, 168(3), 1615–1626.
Abstract: Interspecific differentiation values (G(ST)) between two closely related oak species (Quercus petraea and Q. robur) were compiled across different studies with the aim to explore the distribution of differentiation at the genome level. The study was based on a total set of 389 markers (isozymes, AFLPs, SCARs, microsatellites, and SNPs) for which allelic frequencies were estimated in pairs of populations sampled throughout the sympatric distribution of the two species. The overall distribution of GST values followed an L-shaped curve with most markers exhibiting low species differentiation (G(ST) < 0.01) and only a few loci reaching >10% levels. Twelve percent of the loci exhibited significant G(ST) deviations to neutral expectations, suggesting that selection contributed to species divergence. Coding regions expressed higher differentiation than noncoding regions. Among the 389 markers, 158 could be mapped on the 12 linkage groups of the existing Q. robur genetic map. Outlier loci with large G, values were distributed over 9 linkage groups. One cluster of three outlier loci was found within 0.51 cM; but significant autocorrelation of GST was observed at distances <2 cM. The size and distribution of genomic regions involved in species divergence are discussed in reference to hitchhiking effects and disruptive selection.
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Garcia-Davila, C., Aldana Gomero, D., Renno, J. - F., Diaz Soria, R., Hidalgo Pizango, G., Flores Llampazo, G., et al. (2020). Molecular evidence for three genetic species of Dipteryx in the Peruvian Amazon. Genetica, 148(1), 1–11.
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.
Keywords: 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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Kiaer, L. P., Felber, F., Flavell, A., Guadagnuolo, R., Guiatti, D., Hauser, T. P., et al. (2009). Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L. Genet. Resour. Crop Evol., 56(3), 405–419.
Abstract: Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
Keywords: AFLP; GM co-existence; Gene dispersal; Introgression; Risk assessment; SSAP
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