Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics

Selective logging in Brazil allows for the removal of up to 90% of trees above 50 cm diameter of a given timber species, independent of a species’ life history characteristics or how quickly it will recover. The genetic and demographic effects of selective logging on two Amazonian timber species (Dipteryx odorata Leguminosae, Jacaranda copaia Bignoniaceae) with contrasting ecological and reproductive characteristics were assessed in the same forest. Genetic diversity and gene flow were characterized by genotyping adults and seed sampled before and after logging, using hypervariable microsatellite markers. Overall, there were no short‐term genetic impacts on the J. copaia population, with commercial application of current Brazilian forest management regulations. In contrast, for D. Odorata, selective logging showed a range of genetic impacts, with a 10% loss of alleles, and reductions in siring by pollen from trees within the 546‐ha study area (23–11%) and in the number of pollen donors per progeny array (2.8–1.6), illustrating the importance of the surrounding landscape. Asynchrony in flowering between D. odorata trees led to trees with no breeding partners, which could limit the species reproduction and regeneration under current regulations. The results are summarized with other published studies from the same site and the implications for forest management discussed. The different types and levels of impacts associated with each species support the idea that ecological and genetic information by species, ecological guild or reproductive group is essential in helping to derive sustainable logging guidelines for tropical forests.     

Tree species composition and diversity gradients in white-water forests across the Amazon Basin

Aim Attention has increasingly been focused on the floristic variation within forests of the Amazon Basin. Variations in species composition and diversity are poorly understood, especially in Amazonian floodplain forests. We investigated tree species composition, richness and α diversity in the Amazonian white‐water (várzea) forest, looking particularly at: (1) the flood‐level gradient, (2) the successional stage (stand age), and (3) the geographical location of the forests. Location Eastern Amazonia, central Amazonia, equatorial western Amazonia and the southern part of western Amazonia. Methods The data originate from 16 permanent várzea forest plots in the central and western Brazilian Amazon and in the northern Bolivian Amazon. In addition, revised species lists of 28 várzea forest inventories from across the Amazon Basin were used. Most important families and species were determined using importance values. Floristic similarity between plots was calculated to detect similarity variations between forest types and over geographical distances. To check for spatial diversity gradients, α diversity (Fisher) of the plots was correlated with stand age, longitudinal and latitudinal plot location, and flood‐level gradient. Results More than 900 flood‐tolerant tree species were recorded, which indicates that Amazonian várzea forests are the most species‐rich floodplain forests worldwide. The most important plant families recorded also dominate most Neotropical upland forests, and c. 31% of the tree species listed also occur in the uplands. Species distribution and diversity varied: (1) on the flood‐level gradient, with a distinct separation between low‐várzea forests and high‐várzea forests, (2) in relation to natural forest succession, with species‐poor forests in early stages of succession and species‐rich forests in later stages, and (3) as a function of geographical distance between sites, indicating an increasing α diversity from eastern to western Amazonia, and simultaneously from the southern part of western Amazonia to equatorial western Amazonia. Main conclusions The east‐to‐west gradient of increasing species diversity in várzea forests reflects the diversity patterns also described for Amazonian terra firme. Despite the fine‐scale geomorphological heterogeneity of the floodplains, and despite high disturbance of the different forest types by sedimentation and erosion, várzea forests are dominated by a high proportion of generalistic, widely distributed tree species. In contrast to high‐várzea forests, where floristic dissimilarity increases significantly with increasing distance between the sites, low‐várzea forests can exhibit high floristic similarity over large geographical distances. The high várzea may be an important transitional zone for lateral immigration of terra firme species to the floodplains, thus contributing to comparatively high species richness. However, long‐distance dispersal of many low‐várzea trees contributes to comparatively low species richness in highly flooded low várzea.     

Floodplain lake fish assemblages in the Amazon River: directions in conservation biology

The Neotropical region is renowned for its high biodiversity, and the Amazon River basin contains the highest number of fish species of any river system in the world. In recent years, habitat fragmentation and exploitation of biotic resources have threatened biological integrity and provoked to need for sustainable management and conservation of the Amazon River system. We studied 36 floodplain lakes along 2000 km of the Amazon River. The fish assemblages associated with flood forests are moderately diverse, with low species dominance and reduced populations. To detect nestedness of fish assemblage composition in floodplain lakes, a nested subset analysis was performed on species presence–absence. The incidence matrix (species × lakes) was maximally packed using the Nestedness Temperature Calculator software. The results of ranking lakes and species allow us to establish targets for conservation. Such strategy for sustainable management should be focused on maintaining the Amazonian biodiversity.     

Long-Term Impacts of Forest Ditching on Non-Aquatic Biodiversity: Conservation Perspectives for a Novel Ecosystem

Artificial drainage (ditching) is widely used to increase timber yield in northern forests. When the drainage systems are maintained, their environmental impacts are likely to accumulate over time and along accompanying management, notably after logging when new forest develops on decayed peat. Our study provides the first comprehensive documentation of long-term ditching impacts on terrestrial and arboreal biodiversity by comparing natural alder swamps and second-generation drained forests that have evolved from such swamps in Estonia. We explored species composition of four potentially drainage-sensitive taxonomic groups (vascular plants, bryophytes, lichens, and snails), abundance of species of conservation concern, and their relationships with stand structure in two-ha plots representing four management types (ranging from old growth to clearcut). We found that drainage affected plot-scale species richness only weakly but it profoundly changed assemblage composition. Bryophytes and lichens were the taxonomic groups that were most sensitive both to drainage and timber-harvesting; in closed stands they responded to changed microhabitat structure, notably impoverished tree diversity and dead-wood supply. As a result, natural old-growth plots were the most species-rich and hosted several specific species of conservation concern. Because the most influential structural changes are slow, drainage impacts may be long hidden. The results also indicated that even very old drained stands do not provide quality habitats for old-growth species of drier forest types. However, drained forests hosted many threatened species that were less site type specific, including early-successional vascular plants and snails on clearcuts and retention cuts, and bryophytes and lichens of successional and old forests. We conclude that three types of specific science-based management tools are needed to mitigate ditching effects on forest biodiversity: (i) silvicultural techniques to maintain stand structural complexity; (ii) context-dependent spatial analysis and planning of drained landscapes; and (iii) lists of focal species to monitor and guide ditching practices.     

The Effect of Logging on the Ground-Foraging Ant Community in Eastern Amazonia

In order to determine the suitability of ants as indicator organisms for habitat disruption in tropical forests, we studied the effects of both high and low impact logging on ant communities in northeastern Pará State, in the Brazilian Amazon. We collected ants from logged forests and unlogged forest sites with Winkler bags throughout the 1998 rainy season (January and April) and the following dry season (July and September). Both methods of timber harvesting showed impacts on ant community composition when compared with unlogged forest, although these impacts did not include modifications in total species richness or the relative contribution of each ant subfamily to the total number of species. Instead, logging induced alterations took place at the level of species and genera. A 2-fold reduction in the dominance of ants of the highly diverse genus Pheidole was associated with forest alterations in high-impact logging sites. Thus, logging in Amazonia can be seen to promote species shifts in ant communities, without, however, altering species richness. Ants of the genus Pheidole are potentially useful indicators for forest disturbances resulting from timber extraction.     

Does selective logging stress tropical forest invertebrates? Using fat stores to examine sublethal responses in dung beetles

The increased global demand for tropical timber has driven vast expanses of tropical forests to be selectively logged worldwide. While logging impacts on wildlife are predicted to change species distribution and abundance, the underlying physiological responses are poorly understood. Although there is a growing consensus that selective logging impacts on natural populations start with individual stress‐induced sublethal responses, this literature is dominated by investigations conducted with vertebrates from temperate zones. Moreover, the sublethal effects of human‐induced forest disturbance on tropical invertebrates have never been examined. To help address this knowledge gap, we examined the body fat content and relative abundance of three dung beetle species (Coleoptera: Scarabaeinae) with minimum abundance of 40 individuals within each examined treatment level. These were sampled across 34 plots in a before‐after control‐impact design (BACI) in a timber concession area of the Brazilian Amazon. For the first time, we present evidence of logging‐induced physiological stress responses in tropical invertebrates. Selective logging increased the individual levels of fat storage and reduced the relative abundance of two dung beetle species. Given this qualitative similarity, we support the measurement of body fat content as reliable biomarker to assess stress‐induced sublethal effects on dung beetles. Understanding how environmental modification impacts the wildlife has never been more important. Our novel approach provides new insights into the mechanisms through which forest disturbances impose population‐level impacts on tropical invertebrates.     

A crisis in the making: responses of Amazonian forests to land use and climate change

At least three global-change phenomena are having major impacts on Amazonian forests: (1) accelerating deforestation and logging; (2) rapidly changing patterns of forest loss; and (3) interactions between human land-use and climatic variability. Additional alterations caused by climatic change, rising concentrations of atmospheric carbon dioxide, mining, overhunting and other large-scale phenomena could also have important effects on the Amazon ecosystem. Consequently, decisions regarding Amazon forest use in the next decade are crucial to its future existence.     

Habitat specifity,endemism and the neotropical distribution of Amazonian white‐water floodplain trees

.The Amazon basin is covered by the most species‐rich forests in the world and is considered to house many endemic tree species. Yet, most Amazonian ecosystems lack reliable estimates of their degree of endemism, and causes of tree diversity and endemism are intense matters of debate. We reviewed the spatial distribution of 658 of the most important flood‐tolerant Amazonian white‐water (várzea) tree species across the entire Neotropics by using data from herbaria, floras, inventories and checklists. Our results show that 90% of the várzea tree species are partially or widely distributed across neotropical macro‐regions and biomes. Chi‐square analyses indicated that várzea species richness in non‐várzea macro‐regions was dependent on the flooding gradient and the longitudinal position. Cluster analysis combined with association tests indicated four significant patterns of várzea species distributions depending on species flood‐tolerance (low vs high) and spatial distribution (restricted vs widespread). We predict that the predominance of Andean substrates is the most important factor that determines the distribution of várzea tree species within and beyond the Amazon basin and explains the high floristic similarity to the Orinoco floodplains. Distribution patterns in other extra‐Amazonian macro‐regions are more likely linked to climatic factors, with rainforest climates housing more várzea species than savanna climates. 130 tree species were restricted to South‐American freshwater floodplains, and 68 (> 10%) were endemic to Amazonian várzea. We detected two centers of endemism, one in the western Amazon characterized by low and brief floods, and one in the central Amazon, characterized by high and prolonged floods. Differences in taxonomic composition of endemic centers in the western and central Amazon are the result of different abiotic factors (i.e. flood regimes), as well as the regional species pools from where the species are recruited from. We hypothesize that numerous morphological, physiological and biochemical adaptations permit survival of trees in flooded environments. Furthermore, these adaptations are independently derived across many taxa and result in a highly specialized flora. We attribute higher than expected levels of endemism to the great spatial extent and age of floodplain ecosystems in the Amazon basin, and highlight the role of Amazonian várzea as an potential driver in speciation and diversification processes.     

A profile of palm heart extraction in the Amazon estuary

Many of the processed palm hearts consumed throughout the world are derived from the açaípalm (Euterpe oleraceaMart.)), which grows abundantly in floodplain forests of the Amazon estuary. Palm heart extraction began in the estuary in the 1970s and there are now hundreds of canning factories and some 50 distribution firms in this region. Annual profits of the canning factories range from $30,000 to $50,000 while profits for distribution firms frequently exceed $500,000/year. But there are several indications that this economic boon will be short-lived: factory closings are frequent, palm hearts are much smaller now than in the past, and mortality of palm trees is high in stands subjected to frequent palm heart harvest. However, the açaípalm is well suited for management because of its abundance, rapid growth, and multistemmed life form. Under management, palm hearts can be harvested from the same clump over many years through controlled thinning. The management of açaístands could result in significant long-term savings for palm heart factories. Indeed, açaímanagement may offer one of the best opportunities to date for sustained use of some Amazonian forests.     

Silvicultural intensification for tropical forest conservation

Minimizing the deleterious environmental impacts of logging and other silvicultural treatments is the primary conservation goal in tropical forests managed for timber production. While it is always environmentally beneficial to minimize unnecessary damage, more intensive silviculture should not be discouraged in tropical forests in which regeneration and growth of commercially valuable timber species requires such treatments. Failing to regenerate commercial species may render forests more susceptible to conversion to other, more lucrative land uses. Increasing the intensity of silviculture may also decrease the total area of forest exploited for timber, thereby reducing the impacts of over-hunting, timber theft, wildfires, colonization, and conversion, which are facilitated by the increased accessibility of logged areas.     

Distribution and population structure of four Central Amazonian high-várzea timber species

Amazonian white-water (várzea) floodplains harbor many commercially important timber species which in Brazil are harvested following regulations of the Federal Environmental Agency (IBAMA). Although it is well-known that tree physiology, growth, and species distribution of Amazonian floodplain trees is linked to the heights and durations of the periodical inundations, information about timber stocks and population dynamics is lacking for most tree species. We investigated timber stocks and the population structure of four intensely logged tree species in a western Brazilian várzea forest on an area totaling 7.5 ha. Spatial distribution was investigated in all trees as a function of inundation height and duration and the distance to the river channel, and additionally for saplings (trees <10 cm diameter at breast height––DBH) as a function of the relative photosynthetically active radiation (rPAR). The diameter-class distribution in Hura crepitans and Ocotea cymbarum indicated that populations are subject to density variations that possibly are traced to small-scale flood variability. In all species, saplings concentrated at higher topographic elevations than the mature tree populations, which suggest that the physical ‘escape’ from a flooded environment is an important acclimation to flooding. While Ocotea cymbarum and Guarea guidonia were high-density wood species characterized by random dispersion and a pronounced shade-tolerance, Hura crepitans and Sterculia apetala presented lower wood density, aggregated dispersion, and were more light-demanding. All species presented exploitable stems according to the current harvest regulations, with elevated abundances in comparison to other Amazonian forest types. However, stem densities are below the harvest rates indicating that the harvest regulations are not sustainable. We recommend that the forest management in várzea forests should include specific establishment rates of timber species in dependence of the peculiar site conditions to achieve sustainability.     

Impact of climatic and hydrological disturbances on blackwater floodplain forests in Central Amazonia

Extreme climatic events and anthropic disturbances affect the hydrological regime of Amazonian rivers and connected floodplain forests. This study aims to investigate the impacts of the Balbina hydroelectric power plant on the floodplain forests of the Uatumã River, in the Central Amazon. For this, tree age and diameter increment from the most abundant tree species of three different topographic levels were obtained and analyzed in the affected area downstream of the Balbina dam (Uatumã River) and compared to an undisturbed site (Abacate River, affluent) considering age structure and mean diameter increments between the topographic levels and the two systems. The occurrence of old trees is much lower at the disturbed site compared to the undisturbed system. Especially at the middle topography of the Uatumã site, we observed tree species with high mean diameter increment indicating a strong disturbance. We suggest that the disturbances may be associated with extreme hydro‐climatic events, such as extreme droughts that occurred during the El Niño years 1925/26 and 1982/83 and that these events may increase vulnerability of igapó floodplains to wildfires. Abstract in Portuguese is available with online material.     

The effect of reduced-impact logging on fruit-feeding butterflies in Central Amazon, Brazil

The Amazon region represents more than a half of all tropical forests in the world, and has been threatened by many anthropogenic activities, including several kinds of timber harvesting. The reduced-impact logging (RIL) is considered a less destructive method of timber harvesting, but there is a general lack of information about the effects on Amazonian invertebrates, including butterflies. We investigated the effect of RIL on fruit-feeding butterflies by comparing canopy and understory between an area under RIL and a control area without RIL. The canopy fauna is different and significantly richer than the understory fauna, showing that sampling only the lower strata underestimates the diversity of fruit-feeding butterflies. The effects of RIL were mainly detected in the understory butterfly assemblage, as significant differences were observed in species composition within this stratum. Effects of the RIL regime, which include tree cutting, skid trails and roads openings, are stronger in the understory than in the canopy, explaining the reported differences. Despite the detectable effects of RIL on the composition of fruit-feeding butterfly assemblages, the overall diversity was not affected. A similar pattern has been detected in many other groups, indicating that a noticeable part of the diversity of many taxa could be preserved in areas under RIL management. Therefore, in view of the problems of creating protected areas in the Amazon, RIL is a good alternative to preserve fruit-feeding butterflies and surely many other taxa, and it might be a desirable economic alternative for the region.     

The ecogeographical differentiation of Amazonian inundation forests

Due to the considerable annual fluctuations of water level of the Amazonian rivers, their river banks are fringed with periodically flooded forests of vast extension. The biota of these communities are adapted to annual inundations that can last for more than half a year. Water chemistry is most important for the floristic differentiation of these flooded forests. White water rivers, which carry a rich load of suspended material originating from the erosion of the Andes, have a floristic composition related to that of the noninundatable Amazonian forest. Clear water and black water rivers, which originate in the Amazon Basin or its adjacent crystalline shields, are nutrient-poor and more or less acidic; their flora is related to that of peculiar woodland and savannah vegetation on oligotrophic white sand. The distribution patterns of floodplain species of nutrient-poor waters point to a centre of diversity in the Upper Rio Negro region, and another one in the Guayana lowland. These coincide with diversity centres for species of non-flooded habitats. Hence it seems unlikely that species diversity is directly influenced by pluviosity. The flooded forests have developed biotic interactions with the fish fauna of the Amazon Basin, which are vital for their continued existence. It is assumed that the origin of these habitats, their biota and their interactions dates back long into the Tertiary.     

The fate of Amazonian ecosystems over the coming century arising from changes in climate,atmospheric CO2, and land use

There is considerable interest in understanding the fate of the Amazon over the coming century in the face of climate change, rising atmospheric CO₂ levels, ongoing land transformation, and changing fire regimes within the region. In this analysis, we explore the fate of Amazonian ecosystems under the combined impact of these four environmental forcings using three terrestrial biosphere models (ED2, IBIS, and JULES) forced by three bias‐corrected IPCC AR4 climate projections (PCM1, CCSM3, and HadCM3) under two land‐use change scenarios. We assess the relative roles of climate change, CO₂ fertilization, land‐use change, and fire in driving the projected changes in Amazonian biomass and forest extent. Our results indicate that the impacts of climate change are primarily determined by the direction and severity of projected changes in regional precipitation: under the driest climate projection, climate change alone is predicted to reduce Amazonian forest cover by an average of 14%. However, the models predict that CO₂ fertilization will enhance vegetation productivity and alleviate climate‐induced increases in plant water stress, and, as a result, sustain high biomass forests, even under the driest climate scenario. Land‐use change and climate‐driven changes in fire frequency are predicted to cause additional aboveground biomass loss and reductions in forest extent. The relative impact of land use and fire dynamics compared to climate and CO₂ impacts varies considerably, depending on both the climate and land‐use scenario, and on the terrestrial biosphere model used, highlighting the importance of improved quantitative understanding of all four factors – climate change, CO₂ fertilization effects, fire, and land use – to the fate of the Amazon over the coming century.     

Mortality of developing floodplain forests subjected to a drying climate and water extraction

River regulation and water extraction have altered the hydrology of rivers resulting in substantial changes to forest structure and the dieback of floodplain forests globally. Forest mortality, due to water extraction, is likely to be exacerbated by climate change-induced droughts. In 1965, a plantation trial was established within a natural floodplain forest to examine the effect of planting density on timber production. We used data from this trial to investigate the effect of initial stand density on the structure and dynamics of Eucalyptus camaldulensis (Dehnh.) forests. Highest density stands (8000 trees ha⁻¹) were dominated by many slender trees, mostly<10 cm in diameter, whereas the lowest density stands produced size distributions with a wider range of stem diameters and higher mean and maximum stem diameter. After 1996, the study area experienced a sharp decline in water availability due to a substantial lowering of the water table, reduced flooding frequency, a pronounced rainfall deficit and increased maximum temperatures. The drought coincided with a dramatic increase in mortality in the high-density stands, yet remained little changed in low-density treatments. Our results highlight the importance of initial stand density as a key determinant of the development of forest structure. Early thinning of high-density stands is one component of a broader management approach to mitigate impacts of human-induced drought and water extraction on developing floodplain forests.     

Accumulation and Connectivity of Coarse Woody Debris in Partial Harvest and Unmanaged Relict Forests

When a tree dies, it continues to play an important ecological role within forests. Coarse woody debris (CWD), including standing deadwood (SDW) and downed deadwood (DDW), is an important functional component of forest ecosystems, particularly for many dispersal-limited saproxylic taxa and for metapopulation dynamics across landscapes. Processes, such as natural disturbance or management, modify forest composition and structure, thereby influencing CWD abundance and distribution. Many studies have compared older forests to forests managed with even-aged silvicultural systems and observed a prolonged period of low CWD occurrence after harvesting. With fine-scale spatial data, our study compares the long-term impacts of light partial harvesting on the CWD structure of eastern deciduous hardwood forests. We mapped and inventoried DDW and SDW using variable radius plots based on a 10 m×10 m grid throughout an unmanaged, structurally-complex relict forest and two nearby forests that were partially harvested over 46 years ago. The relict stand had significantly larger individual pieces and higher accumulations of DDW and SDW than both of the partially harvested stands. Connectivity of CWD was much higher in the relict stand, which had fewer, larger patches. Larger pieces and higher proportion of decay-resistant species (e.g. Quercus spp.) in the relict forest resulted in slower decomposition, greater accumulation and increased connectivity of CWD. Partial harvests, such that occur with selection forestry, are generally considered less disruptive of ecosystem services, but this study highlights the long-term impacts of even light partial harvests on CWD stocks and distribution. When planning harvesting events, forest managers should also consider alternative methods to ensure the sustainability of deadwood resources and function.     

Three fishes in one: cryptic species in an Amazonian floodplain forest specialist

Accurately describing biodiversity in tropical regions such as Amazonia is difficult because of insufficient morphological inventories and the lack of studies on the distribution of genetic diversity. Aquatic organisms from Amazonian flooded forests are generally expected to move laterally along the forests during the annual inundation cycle, a behaviour that should promote admixture of populations and reduce within‐drainage speciation. We used an unprecedented fine‐scale sampling effort and multiple DNA markers to quantify region‐wide population differentiation in an Amazonian floodplain forest specialist, the black‐wing hatchet fish Carnegiella marthae ( Myers, 1927 ). Our study revealed three previously unsuspected and ancient cryptic species of black‐wing hatchet fish in the Rio Negro floodplain (RNF), in central Amazonia. Two species produce occasional first‐generation hybrids. The third and rarer species, although found in extreme sympatry with another species, appears to be reproductively isolated, and also differs in external morphology and dentition. Our findings have important implications for guiding conservation management because C. marthae is harvested commercially in the RNF ornamental fishery. They also suggest that the diversity of Amazonian ichthyofauna is vastly underestimated, including that found in landscapes lacking contemporary barriers to account for population divergence and speciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 391–403.     

Long-term impacts of selective logging on two Amazonian tree species with contrasting ecological and reproductive characteristics: inferences from Eco-gene model simulations

The impact of logging and subsequent recovery after logging is predicted to vary depending on specific life history traits of the logged species. The Eco-gene simulation model was used to evaluate the long-term impacts of selective logging over 300 years on two contrasting Brazilian Amazon tree species, Dipteryx odorata and Jacaranda copaia. D. odorata (Leguminosae), a slow growing climax tree, occurs at very low densities, whereas J. copaia (Bignoniaceae) is a fast growing pioneer tree that occurs at high densities. Microsatellite multilocus genotypes of the pre-logging populations were used as data inputs for the Eco-gene model and post-logging genetic data was used to verify the output from the simulations. Overall, under current Brazilian forest management regulations, there were neither short nor long-term impacts on J. copaia. By contrast, D. odorata cannot be sustainably logged under current regulations, a sustainable scenario was achieved by increasing the minimum cutting diameter at breast height from 50 to 100 cm over 30-year logging cycles. Genetic parameters were only slightly affected by selective logging, with reductions in the numbers of alleles and single genotypes. In the short term, the loss of alleles seen in J. copaia simulations was the same as in real data, whereas fewer alleles were lost in D. odorata simulations than in the field. The different impacts and periods of recovery for each species support the idea that ecological and genetic information are essential at species, ecological guild or reproductive group levels to help derive sustainable management scenarios for tropical forests.     

Influence of Deforestation,Logging, and Fire on Malaria in the Brazilian Amazon

Malaria is a significant public health threat in the Brazilian Amazon. Previous research has shown that deforestation creates breeding sites for the main malaria vector in Brazil, Anopheles darlingi, but the influence of selective logging, forest fires, and road construction on malaria risk has not been assessed. To understand these impacts, we constructed a negative binomial model of malaria counts at the municipality level controlling for human population and social and environmental risk factors. Both paved and unpaved roadways and fire zones in a municipality increased malaria risk. Within the timber production states where 90% of deforestation has occurred, compared with areas without selective logging, municipalities where 0–7% of the remaining forests were selectively logged had the highest malaria risk (1.72, 95% CI 1.18–2.51), and areas with higher rates of selective logging had the lowest risk (0.39, 95% CI 0.23–0.67). We show that roads, forest fires, and selective logging are previously unrecognized risk factors for malaria in the Brazilian Amazon and highlight the need for regulation and monitoring of sub-canopy forest disturbance.