Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Background: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal's life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.Results: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.Conclusions: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle. © 2013 Mokry et al.; licensee BioMed Central Ltd.

Partitioning of net primary production in Eucalyptus and Acacia stands and in mixed-species plantations: Two case-studies in contrasting tropical environments

The introduction of nitrogen fixing species (NFS) in fast-growing tree plantations is an alternative option to reduce fertilizer inputs. However, the success of mixed-species plantations depends on the balance between positive interactions among species (resulting from facilitation and/or complementarity) and the negative effects of interspecific competition.Using a carbon budget approach and coupling measurements of standing biomass, aboveground litterfall and soil CO2 efflux, we assessed the influence of replacing half of eucalypt trees by Acacia mangium on total belowground carbon flux (TBCF), net primary production (NPP) and its partitioning between above- and belowground growth at two tropical sites in Brazil (Itatinga) and in Congo (Kissoko) exhibiting contrasting climates, edaphic conditions and wood productions.Annual soil CO2 efflux (FS) was significantly lower in the acacia monocultures than in eucalypt monocultures and mixed-species stands at both sites. Annual FS was significantly lower at Itatinga compared to Kissoko for all stands while TBCF was significantly lower in the eucalypt stands only. In the eucalypt monocultures we found a significantly lower aboveground NPP (ANPP) and wood production (wood NPP) at Kissoko compared to Itatinga that was almost fully balanced by a significantly higher belowground NPP (BNPP), leading to similar NPP. Similarly, acacia monocultures exhibited significantly higher ANPP and wood NPP at Itatinga than at Kissoko. The mixed-species stands exhibited a significantly lower wood NPP and ANPP than the eucalypt monocultures at the Brazilian site while NPP of the mixture was not significantly different than the average NPP of the two monocultures. At the Congolese site, NPP of the mixture was significantly higher than the average NPP of the two monocultures. NPP was similar in the mixed-species stand and the eucalypt monoculture with a significantly lower partitioning of NPP to belowground production, leading to a one third higher wood biomass at harvest in the mixed-species stand.A positive effect of growing eucalypts with the nitrogen fixing acacia trees on stand wood production occurred at Kissoko but not at Itatinga. Mixed-species plantations with NFS can be advocated at sites where the productive gains resulting from nitrogen fixation are not compromised by other resource limitations. © 2012 Elsevier B.V.

Seed dispersal by the lek-forming white-bearded manakin (Manacus manacus, Pipridae) in the Brazilian Atlantic forest

The movement patterns of males, females and juveniles of lekking species often differ due to differences in the commitment to lek activities, which may lead to differences in the spatial distribution and dispersal distances of seeds they eat. By sampling seeds in three lek and non-lek areas of the white-bearded manakin (Manacus manacus), we tested whether this lekking species increased the abundance and species richness of seeds in lek areas and, at a finer scale, in 21 displaying courts within lek areas. Combining data on seed defecation or regurgitation rates by free-ranging individuals, the number of seeds in droppings or regurgitations of mist-netted birds, and the distances travelled by birds equipped with radio-transmitters, we estimated the potential spatial distribution of seeds generated by six resident males and six females or juveniles during the morning peak of lek activity and when lek activity decreased in the afternoon. There was no difference in the species richness (46 and 44 morphospecies, respectively) and abundance of seeds (15.4 ± 7.3 seeds and 14.0 ± 1.1 seeds, respectively) between lek and non-lek areas. Within leks both parameters increased in courts (45 spp., 17.6 ± 14 seeds) compared with non-court sites (22 spp., 1.9 ± 1.8 seeds), likely as a consequence of the longer time spent by resident males in perches in or near display courts. Distances moved by juveniles and females per 60-min period (183 ± 272 m) were greater than resident males (42.6 ± 22.0 m) in the mornings, while the opposite happened in the afternoons (55.2 ± 40.7 m and 157 ± 105 m, respectively). We conclude that the spatial aggregation of seeds in lek areas of M. manacus occurs at the court level, and the spatial distribution of deposited seeds varies with manakin lekking status and the daily period of foraging. © Cambridge University Press 2013.

Reproductive phenology and fruit production on a land bridge island in the brazilian atlantic forest

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Frugivoria e efetividade de dispersão de sementes dos últimos grandes frugívoros da Mata Atlântica: a anta (Tapirus terrestris) e o muriqui (Brachyteles arachnoides)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Preferência alimentar por insetos aquáticos em espécies de peixes de riacho tropical

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Progressive recovery of a tropical deforested stream community after a flash flood

AIM: In this study, we evaluated and compared community attributes from a tropical deforested stream, located in a pasture area, in a period before (PRED I) and three times after (POSD I, II, and III) a flash flood, in order to investigate the existence of temporal modifications in community structure that suggests return to conditions previous to the flash flood. METHODS: Biota samples included algae, macrophytes, macroinvertebrates, and fish assemblages. Changes in stream physical structure we also evaluated. Similarity of the aquatic biota between pre and post-disturbance periods was examined by exploratory ordination, known as Non-Metric Multidimensional Scaling associated with Cluster Analysis, using quantitative and presence/absence Bray-Curtis similarity coefficients. Presence and absence data were used for multivariate correlation analysis (Relate Analysis) in order to investigate taxonomic composition similarity of biota between pre and post-disturbance periods. RESULTS: Our results evidenced channel simplification and an expressive decrease in richness and abundance of all taxa right after the flood, followed by subsequent increases of these parameters in the next three samples, indicating trends towards stream community recovery. Bray-Curtis similarity coefficients evidenced a greater community structure disparity among the period right after the flood and the subsequent ones. Multivariate correlation analysis evidenced a greater correlation between macroinvertebrates and algae/macrophytes, demonstrating the narrow relation between their recolonization dynamics. CONCLUSIONS: Despite overall community structure tended to return to previous conditions, recolonization after the flood was much slower than that reported in literature. Finally, the remarkably high flood impact along with the slow recolonization could be a result of the historical presence of anthropic impacts in the region, such as siltation, riparian forest complete depletion, and habitat simplification, which magnified the effects of a natural disturbance.

Leaf synchrony and insect herbivory among tropical tree habitat specialists

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Amazon forest biomass density maps: tackling the uncertainty in carbon emission estimates

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Sandflies (Diptera, Psychodidae) from forest areas in Botucatu municipality, central western Sao Paulo State, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

High abundance of an exotic amphipod indicates disturbance in tropical rainforests

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of the Tropical Rainfall Measuring Mission 3B43 product over an inland area in Brazil and the effects of satellite boost on rainfall estimates

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A new probabilistic canopy dynamics model (SLCD) that is suitable for evergreen and deciduous forest ecosystems

There are strong uncertainties regarding LAI dynamics in forest ecosystems in response to climate change. While empirical growth & yield models (G&YMs) provide good estimations of tree growth at the stand level on a yearly to decennial scale, process-based models (PBMs) use LAI dynamics as a key variable for enabling the accurate prediction of tree growth over short time scales. Bridging the gap between PBMs and G&YMs could improve the prediction of forest growth and, therefore, carbon, water and nutrient fluxes by combining modeling approaches at the stand level.Our study aimed to estimate monthly changes of leaf area in response to climate variations from sparse measurements of foliage area and biomass. A leaf population probabilistic model (SLCD) was designed to simulate foliage renewal. The leaf population was distributed in monthly cohorts, and the total population size was limited depending on forest age and productivity. Foliage dynamics were driven by a foliation function and the probabilities ruling leaf aging or fall. Their formulation depends on the forest environment.The model was applied to three tree species growing under contrasting climates and soil types. In tropical Brazilian evergreen broadleaf eucalypt plantations, the phenology was described using 8 parameters. A multi-objective evolutionary algorithm method (MOEA) was used to fit the model parameters on litterfall and LAI data over an entire stand rotation. Field measurements from a second eucalypt stand were used to validate the model. Seasonal LAI changes were accurately rendered for both sites (R-2 = 0.898 adjustment, R-2 = 0.698 validation). Litterfall production was correctly simulated (R-2 = 0.562, R-2 = 0.4018 validation) and may be improved by using additional validation data in future work. In two French temperate deciduous forests (beech and oak), we adapted phenological sub-modules of the CASTANEA model to simulate canopy dynamics, and SLCD was validated using LAI measurements. The phenological patterns were simulated with good accuracy in the two cases studied. However, IA/max was not accurately simulated in the beech forest, and further improvement is required.Our probabilistic approach is expected to contribute to improving predictions of LAI dynamics. The model formalism is general and suitable to broadleaf forests for a large range of ecological conditions. (C) 2014 Elsevier B.V. All rights reserved.

Effects of litter manipulation in a tropical Eucalyptus plantation on leaching of mineral nutrients, dissolved organic nitrogen and dissolved organic carbon

Although many studies have shown that soil solution chemistry can be a reliable indicator of biogeochemical cycling in forest ecosystems, the effects of litter manipulations on the fluxes of dissolved elements in gravitational soil solutions have rarely been investigated. We estimated the fluxes of NH4-N, NO3-N, K, Ca, Mg, Na, Cl, dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) over the first two years after re-planting Eucalyptus trees in the coastal area of Congo. Two treatments were replicated in two blocks after clear-cutting 7-year-old stands: in treatment R, all the litter above the mineral soil was removed before planting, and in a double slash (DS) treatment, the amount of harvest residues was doubled. The soil solutions were sampled down to a depth of 4 m and the water fluxes were estimated using the Hydrus 1D model parameterized from soil moisture measurements in 4 plots. Isotopic and spectroscopic analytical techniques were used to assess the changes in dissolved organic matter (DOM) properties throughout the transfer in the soil. The first year after planting, the fluxes of NH4-N, K, Ca, Mg, Na, Cl and DOC in the topsoil of the DS treatment were 2-5 times higher than in R, which showed that litter was a major source of dissolved nutrients. Nutrient fluxes in gravitational solutions decreased sharply in the second year after planting, irrespective of the soil depth, as a result of intense nutrient uptake by Eucalyptus trees. Losses of dissolved nutrients were noticeably low in these Eucalyptus plantations despite a low cation exchange capacity, a coarse soil texture and large amounts of harvest residues left on-site at the clear cut in the DS treatment. All together, these results clarified the strong effect of litter manipulation observed on eucalypt growth in Congolese sandy soils. DOM fluxes, as well as changes in delta C-13, C:N and aromaticity of DOM throughout the soil profile showed that the organic compounds produced in the litter layer were mainly consumed by microorganisms or retained in the topsoil. Below a depth of 15 cm, most of the DOC and the DON originated from the first 2 cm of the soil and the exchanges between soil solutions and soil organic matter were low. (C) 2014 Elsevier B.V. All rights reserved.

Rapid Assessment of Seed Removal and Frugivore Activity as a Tool for Monitoring the Health Status of Tropical Forests

Ecological processes in tropical forests are being affected at unprecedented rates by human activities. Yet, the continuity of ecological functions like seed dispersal is crucial for forest regeneration. It thus becomes increasingly urgent to be able to rapidly assess the health status of these processes in order to take appropriate management measures. We tested a method to rapidly evaluate seed removal rates on two animal-dispersed tree species, Virola kwatae and V.michelii (Myristicaceae), at three sites in French Guiana with increasing levels of anthropogenic disturbance. We counted fallen fruits, fruit valves, and seeds of each focal fruiting tree in a single 1m2 quadrat, and calculated two indices: the proportion of seeds removed and the proportion of fruits opened by mammals. They both provide an indirect and rapid assessment of frugivore activity. Our results showed a significant decrease in the proportion of removed seeds (16%) and fruits opened (19%) at the most impacted site in comparison with the other two sites (79% for seeds, 60% and 35% for fruits). This testifies to an increased impoverishment of the primate and toucan communities at the disturbed sites. This standardized protocol provides fast information about the health status of the community of seed dispersers and predators and of their seed removal services. It is time- and cost-effective and is not species-specific, allowing comparisons among sites or over time. We suggest using it with the pantropical Myristicaceae and any other capsule-producing family to rapidly assess the health status of seed removal processes across the tropics.