Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism

The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world''s richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.     

Beyond Reserves: A Research Agenda for Conserving Biodiversity in Human-modified Tropical Landscapes

To truly understand the current status of tropical diversity and to forecast future trends, we need to increase emphasis on the study of biodiversity in rural landscapes that are actively managed or modified by people. We present an integrated landscape approach to promote research in human-modified landscapes that includes the effects of landscape structure and dynamics on conservation of biodiversity, provision of ecosystem services, and sustainability of rural livelihoods. We propose research priorities encompassing three major areas: biodiversity, human–environment interactions, and restoration ecology. We highlight key areas where we lack knowledge and where additional understanding is most urgent for promoting conservation and sustaining rural livelihoods. Finally, we recommend participatory and multidisciplinary approaches in research and management. Lasting conservation efforts demand new alliances among conservation biologists, agroecologists, agronomists, farmers, indigenous peoples, rural social movements, foresters, social scientists, and land managers to collaborate in research, co-design conservation programs and policies, and manage human-modified landscapes in ways that enhance biodiversity conservation and promote sustainable livelihoods.     

Co‐benefits of biodiversity and carbon sequestration from regenerating secondary forests in the Philippine uplands: implications for forest landscape restoration

Shifting cultivation is a widespread practice in tropical forested areas that policy makers often regard as the major cause of forest degradation. Secondary fallow forests regrowing after shifting cultivation are generally not viewed as suitable for biodiversity conservation and carbon retention. Drawing upon our research in the Philippines and other relevant case studies, we compared the biodiversity and carbon sequestration in recovering secondary forests after shifting cultivation to other land uses that commonly follow shifting cultivation. Regenerating secondary forests had higher biodiversity than fast growing timber plantations and other restoration options available in the area. Some old plantations, however, provided carbon benefits comparable the old growth forest, although their biodiversity was less than that of the regenerating forests. Our study demonstrates that secondary forests regrowing after shifting cultivation have a high potential for biodiversity and carbon sequestration co‐benefits, representing an effective strategy for forest management and restoration in countries where they are common and where the forest is an integral part of rural people's livelihoods. We discuss the issues and potential mechanisms through which such dynamic land use can be incorporated into development projects that are currently financing the sustainable management, conservation, and restoration of tropical forests.     

Fine-scale spatial genetic structure of Dalbergia nigra (Fabaceae), a threatened and endemic tree of the Brazilian Atlantic Forest

The Atlantic Forest is one of the most diverse ecosystems in the world and considered a hotspot of biodiversity conservation. Dalbergia nigra (Fabaceae) is a tree endemic to the Brazilian Atlantic Forest, and has become threatened due to overexploitation of its valuable timber. In the present study, we analyzed the genetic diversity and fine-scale spatial genetic structure of D. nigra in an area of primary forest of a large reserve. All adult individuals (N = 112) were sampled in a 9.3 ha plot, and genotyped for microsatellite loci. Our results indicated high diversity with a mean of 8.6 alleles per locus, and expected heterozygosity equal to 0.74. The co-ancestry coefficients were significant for distances among trees up to 80 m. The Sp value was equal to 0.017 and indirect estimates of gene dispersal distances ranged from 89 to 144 m. No strong evidence of bottleneck or effects of human-disturbance was found. This study highlights that long-term efforts to protect a large area of Atlantic Forest have been effective towards maintaining the genetic diversity of D. nigra. The results of this study are important towards providing a guide for seed collection for ex-situ conservation and reforestation programmes of this threatened species.     

Fine-scale sites of global conservation importance in the Atlantic forest of Brazil

The Brazilian Atlantic Forest is a highly threatened biodiversity hotspot that has been the subject of several complementary conservation assessments and priority-setting initiatives in the last 30 years. Results of these initiatives have relied on distinct types of distribution data for biodiversity features and differ in the objectivity and repeatability of their methodologies. Here we refine earlier priority-setting exercises using the key biodiversity areas (KBA) approach. We evaluate how well these KBAs are represented in the existing protected areas system, prioritize among them, and analyze critical aspects of the KBA methodology in the Brazilian Atlantic Forest context, such as its ability to guide specific conservation strategies. Building upon an extensive database with 1,636 species records and 122 previously identified Important Bird Areas, we demonstrate that conservation assessments in highly fragmented landscapes may be benefited by high resolution species data as is required by the KBA process. We identify 538 KBAs for 141 globally threatened vertebrate species. Prioritizing among these KBA, we highlight the 24 most irreplaceable sites for terrestrial vertebrate species conservation in the Atlantic Forest, based on existing data.     

Ecological outcomes and livelihood benefits of community‐managed agroforests and second growth forests in Southeast Brazil

The Forest and Landscape Restoration movement has emerged as an approach to reconcile biodiversity conservation, ecosystem services provisioning and human well‐being in degraded landscapes, but little is known so far about the potential of different reforestation methods to achieve these objectives. Based on this gap, we assessed the ecological outcomes and local livelihood benefits of community‐managed agroforests and second growth forests to assist natural regeneration in the coastal Atlantic Forest of Brazil. We investigated and compared agroforests and secondary forests according to their structure and floristic composition in 51 circular plots of 314 m², their role in supporting local livelihoods (45 semi‐structured interviews) and the use and cultural importance of plant species (61 interviews). Agroforests and, more remarkably, managed secondary forests (1) re‐established a well‐developed forest structure, with a higher density of tree‐sized individuals and similar basal area compared to nearby old growth forests; (2) were composed by a rich array of native species, including five threatened species, but had lower species richness than old growth remnants; and (3) improved local livelihoods by supplying market valuable and culturally important plants, including 231 native ethnospecies. Overall, local production systems showed remarkable potential to engage smallholders of developing tropical countries in Forest and Landscape Restoration and contribute to achieve its overall goals. We advocate the promotion of these systems as effective Forest and Landscape Restoration approaches in multi‐scale programs and policies.     

Conservation in tropical landscape mosaics: the case of the cacao landscape of southern Bahia, Brazil

A recent debate has contrasted two conservation strategies in agricultural landscapes; either “land sparing” farm development combining intensive production practices with forest set-asides, or “wildlife-friendly” farming with greater on-farm habitat value but lower yields. We argue that in established mosaic landscapes including old cacao production regions where natural forest has already been reduced to relatively small fragments, a combination of both strategies is needed to conserve biodiversity. After reviewing the evidence for the insufficiency of either strategy alone if applied to such landscapes, the paper focuses on the cacao production landscape of southern Bahia, Brazil, once the world’s second largest cacao producer. Here, small remaining areas of Atlantic Forest are embedded in a matrix dominated by traditional cacao agroforests, resulting in a landscape mosaic that has proven favorable to the conservation of the region’s high biodiversity. We show that current land use dynamics and public policies pose threats but also offer opportunities to conservation and describe a three-pronged landscape conservation strategy, consisting of (i) expansion of the protected areas system, (ii) promotion of productive yet biodiversity-friendly cacao farming practices, and (iii) assistance to land users to implement legally mandated on-farm reserves and voluntary private reserves. We discuss recent experiences concerning the implementation of this strategy, discuss likely future scenarios, and reflect on the applicability of the Bahian experience to biodiversity rich cacao production regions elsewhere in the tropics.     

Use and knowledge of plants by “<Emphasis Type="Italic">Quilombolas</Emphasis>” as subsidies for conservation efforts in an area of Atlantic Forest in Espírito Santo State,Brazil

The present work was undertaken in the Cachoeira do Retiro “Quilombola” community, located in the municipality of Santa Leopoldina (20°06′04″S × 40°31′47″W), in Espírito Santo State, Brazil. We expected to encounter high levels of ethnobotanical knowledge in the community due to its distance from the principal local urban center and its localization in a region of high biodiversity. Field work was undertaken between August 2005 and August 2006, employing semi-structured interviews, participant observation, artifact-interviews, as well as the “walk-in-the-forest” technique in the company of a local specialist. Ten additional informants participated in the research (seven women and three men with ages between 42 and 84) who were identified using the “snow-ball” method. A total of 192 ethnospecies belonging to 188 distinct plant taxa were cited (with 59% being native to the Atlantic Forest biome) and were classified into the following use-categories: medicinal (52%), food (34%), construction (18%), technology (10%), ritualistic (5%), ornamental (5%), and fuelwoods (2%). The plants with the greatest Use-Values were Attalea humilis (1.3) and Polyandrococos caudescens (1.1). The Diversity Index of the community’s ethnobotanical knowledge (5.12 nats) was found to be higher than seen in other ethnobotanical studies undertaken in the Atlantic Forest. Using a methodology for determining conservation priorities it was found that 17 of the 49 species analyzed should be examined more closely in studies that could help guarantee the continuity of their populations in the local forest fragment in light of their low density and intense utilization by the Retiro Quilombola community.     

Stability or breakdown under climate change? A key group of woody bamboos will find suitable areas in its richness center

Bamboos play an important role in forest dynamics, but management strategies are needed to avoid monodominance. Understanding how climate change would influence the geographic distribution of bamboos could provide management tools for habitat conservation, as well as prevent the expansion of this group. We investigated the distribution patterns of Merostachys species that are endemic to the Brazilian Atlantic Forest, under current and future climate scenarios. We obtained occurrence records based on field collection, herbaria data and online databases. We used the Maxent algorithm to model potential distribution. Future scenarios considered the IPCC forecasted climate for 2070. Our models showed that a reduction in suitable areas for Merostachys species will likely occur, but the existence of suitable areas under climate changes in the Brazilian Atlantic Forest indicates climatic stability in some areas of occurrence of these species in their richness center. Since the fact that in places with local dominance of woody bamboos there is a decrease in the diversity of other plant species, the occurrence of Merostachys throughout the suitable areas may represent risks to biodiversity conservation. Investigations of the synergistic effects of climate change and the local dominance of woody bamboos are required. Therefore, management measures may be very important to control the occurrence of woody bamboos in the Brazilian Atlantic Forest, mainly in climatically stable areas.     

A forest habitat network for the Atlantic Oakwoods in Highland region,Scotland

Summary

The need to conserve biological diversity and ensure the future viability and integrity of Atlantic oakwoods in a fragmented landscape has led to strategies that facilitate a more holistic view of biodiversity conservation across extensive areas. The Scottish Forestry Strategy contains a major aspiration to develop forest habitat networks through the restoration and improvement of existing woodland and the expansion of new woodland. The Forest Research landscape ecology model BEETLE (Biological and Environmental Evaluation Tools for Landscape Ecology) uses a focal species approach to assess the functional connectivity of habitat within the wider landscape matrix. This model has been used to predict the current habitat network for Atlantic oakwood specialists in the Highland region of Scotland. The analysis outputs are presented with an approach to help practitioners and planners visualise the opportunities to target expansion, conversion or restoration of Atlantic oakwoods and their intrinsic biodiversity.     

The Cashew Frontier in Guinea-Bissau,West Africa: Changing Landscapes and Livelihoods

Guinea-Bissau farmers are replacing shifting cultivation with cashew (Anacardium occidentale) orchards in response to international and national economic and conservation policies, local social changes and perceived increasing climate instability. However, changes from relative food self-provisioning to full dependence on one cash crop and from a complex mosaic of agricultural fields, fallows and forest patches to a homogenous landscape of cashew agroforests impacts both the natural environment and livelihoods. This article on the demise of shifting cultivation in the tropics contributes to the growing body of scholarship on land use-cover change (LUCC) and its multiplex global, national and local drivers, varying across time and space. Further, we argue that instead of adopting an approach exclusively focused on parks, conservation-oriented external interventions should engage with farmers in the development of innovations that both preserve forest ecosystems and enhance food security.     

Crop Expansion and Conservation Priorities in Tropical Countries

Expansion of cropland in tropical countries is one of the principal causes of biodiversity loss, and threatens to undermine progress towards meeting the Aichi Biodiversity Targets. To understand this threat better, we analysed data on crop distribution and expansion in 128 tropical countries, assessed changes in area of the main crops and mapped overlaps between conservation priorities and cultivation potential. Rice was the single crop grown over the largest area, especially in tropical forest biomes. Cropland in tropical countries expanded by c. 48,000 km² per year from 1999–2008. The countries which added the greatest area of new cropland were Nigeria, Indonesia, Ethiopia, Sudan and Brazil. Soybeans and maize are the crops which expanded most in absolute area. Other crops with large increases included rice, sorghum, oil palm, beans, sugar cane, cow peas, wheat and cassava. Areas of high cultivation potential—while bearing in mind that political and socio-economic conditions can be as influential as biophysical ones—may be vulnerable to conversion in the future. These include some priority areas for biodiversity conservation in tropical countries (e.g., Frontier Forests and High Biodiversity Wilderness Areas), which have previously been identified as having ‘low vulnerability’, in particular in central Africa and northern Australia. There are also many other smaller areas which are important for biodiversity and which have high cultivation potential (e.g., in the fringes of the Amazon basin, in the Paraguayan Chaco, and in the savanna woodlands of the Sahel and East Africa). We highlight the urgent need for more effective sustainability standards and policies addressing both production and consumption of tropical commodities, including robust land-use planning in agricultural frontiers, establishment of new protected areas or REDD+ projects in places agriculture has not yet reached, and reduction or elimination of incentives for land-demanding bioenergy feedstocks.     

Effectiveness of Protected Areas for biodiversity conservation: Mammal occupancy patterns in the Iguaçu National Park,Brazil

Protected areas – widely recognized as the main strategy for biodiversity conservation – have greatly expanded, covering ∼15% of the Earth; however, we still lack detailed information on biodiversity to evaluate their effectiveness. This is particularly urgent for biodiversity hotspots where protected areas are islands within human modified landscapes. We focus on mammals of the Iguaçu National Park – one of the most important parks in the Atlantic Forest hotspot – to evaluate the effectiveness of protected areas in conserving biodiversity. We monitored 300 km² with 37 cameras traps during five years to assess if (1) species occupancy declined over time, and (2) if species occupancy/detectability are spatially associated with illegal hunting, proximity to tourism infrastructure and distance from the edge, estimating the proportion of the park where these negative effects are detected. Many species that are rare in most Atlantic Forest remnants presented high occupancy within the park, and no decline in occupancy was observed over time. However, the distribution of 11 species was spatially associated primarily with the distance from the edge and proximity to tourism infrastructure, resulting in a decline, across half of the park area, from 13 to 23% in occupancy and from 19 to 35% in detectability (values averaged among species). These negative effects should be even stronger on smaller protected areas, which are the majority in highly altered hotspots. Re-establishing and properly managing buffer zones and restricting tourism to localized areas are essential to ensure the effectiveness of protected areas for biodiversity conservation.     

How may agricultural matrix intensification affect understory birds in an Atlantic Forest landscape? A qualitative model on stochasticity and immigration

Understanding how different approaches of matrix management affect organisms that inhabit natural patches is crucial for biological conservation. Considering that great part of the tropical area is composed of agricultural land and that most of the land use is either intensified or on the verge to be, a relevant question is: how may agricultural intensification of the landscape matrix affect the population dynamics of understory birds? This paper describes a qualitative model based on the Qualitative Process Theory and implemented in Garp3 to provide answers to this question. We built a model using four species of endemic passerine birds in order to evaluate the case in an Atlantic Forest area, a biodiversity hotspot. The model describes a landscape composed of an extinction-resistant source patch and one target forest patch where stochastic events occur. If permeability of the matrix exceeds a given species-specific threshold, propagules coming from the source reach the target patch. Agriculture intensification affects the matrix spatial structure and reduces permeability to forest birds, thus reduces rescue effect. Additionally, we assume that some species may use the matrix as a supplementary habitat for feeding and that matrix management may affect the resource base for those species. Simulation results suggest that, if agriculture intensification continues to threat the Atlantic Forest biome, populations of sensitive species (Xiphorhynchus fuscus and Sclerurus scansor) that exist in the small forest patches (which is true for most forest remnants) will be highly susceptible to local extinctions and without further re-colonization.     

Secondary forest fragments offer important carbon and biodiversity cobenefits

Tropical forests store large amounts of carbon and high biodiversity, but are being degraded at alarming rates. The emerging global Forest and Landscape Restoration (FLR) agenda seeks to limit global climate change by removing carbon dioxide from the atmosphere through the growth of trees. In doing so, it may also protect biodiversity as a free cobenefit, which is vital given the massive shortfall in funding for biodiversity conservation. We investigated whether natural forest regeneration on abandoned pastureland offers such cobenefits, focusing for the first time on the recovery of taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD) of trees, including the recovery of threatened and endemic species richness, within isolated secondary forest (SF) fragments. We focused on the globally threatened Brazilian Atlantic Forest, where commitments have been made to restore 1 million hectares under FLR. Three decades after land abandonment, regenerating forests had recovered ~20% (72 Mg/ha) of the above‐ground carbon stocks of a primary forest (PF), with cattle pasture containing just 3% of stocks relative to PFs. Over this period, SF recovered ~76% of TD, 84% of PD and 96% of FD found within PFs. In addition, SFs had on average recovered 65% of threatened and ~30% of endemic species richness of primary Atlantic forest. Finally, we find positive relationships between carbon stock and tree diversity recovery. Our results emphasize that SF fragments offer cobenefits under FLR and other carbon‐based payments for ecosystem service schemes (e.g. carbon enhancements under REDD+). They also indicate that even isolated patches of SF could help to mitigate climate change and the biodiversity extinction crisis by recovering species of high conservation concern and improving landscape connectivity.     

Systematics of Spiny Predatory Katydids (Tettigoniidae: Listroscelidinae) from the Brazilian Atlantic Forest Based on Morphology and Molecular Data

Listroscelidinae (Orthoptera: Tettigoniidae) are insectivorous Pantropical katydids whose taxonomy presents a long history of controversy, with several genera incertae sedis. This work focused on species occurring in the Brazilian Atlantic Forest, one of the world''s most threatened biomes. We examined material deposited in scientific collections and visited 15 conservation units from Rio de Janeiro to southern Bahia between November 2011 and January 2012, catching 104 specimens from 10 conservation units. Based on morphological and molecular data we redefined Listroscelidini, adding a new tribe, new genus and eight new species to the subfamily. Using morphological analysis, we redescribed and added new geographic records for six species, synonymized two species and built a provisional identification key for the Atlantic Forest Listroscelidinae. Molecular results suggest two new species and a new genus to be described, possibly by the fission of the genus Hamayulus. We also proposed a 500 bp region in the final portion of the COI to be used as a molecular barcode. Our data suggest that the Atlantic Forest Listroscelidinae are seriously endangered, because they occur in highly preserved forest remnants, show high rates of endemism and have a narrow geographic distribution. Based on our results, we suggest future collection efforts must take into account the molecular barcode data to accelerate species recognition.     

Linking beta diversity patterns to protected areas: lessons from the Brazilian Atlantic Rainforest

Understanding the processes that drive patterns of beta diversity is crucial for planning conservation policies and for designing networks of protected area (PAs). Beta diversity can be decomposed into two components: 1—species turnover, the replacement of species by others resulting in a low proportion of shared species; 2—species nestedness—the result of differences in species richness, when a poorer community is a subset of species from a richer community. We aimed to evaluate beta diversity patterns and how they are represented in the network of PAs in southern Brazilian, regarding three forest types: Atlantic Forest s.s., Araucaria Forest, and Seasonal Forest. Beta diversity was partitioned into the turnover and nestedness components. Additionally, we examined spatial patterns of site similarity using distance decay curves. Beta diversity was mainly caused by species turnover (approx. 86%), with only a small contribution of nestedness (approx. 5%) in all three forests types. The patterns of distance decay curves revealed that even at small distances (50–100 km), we found a considerable decrease in similarities, reinforcing turnover patterns. As turnover brought the larger contribution to beta diversity, additional conservation efforts must target an increase in the number of PAs, that should be spread across each one of the regions, to maximize the protection of species diversity. Most of the PAs are currently limited to the eastern region and prioritize the Atlantic Forest s.s. Thus Araucaria Forest and Seasonal Forest should deserve special priority in new conservation actions, as they also contain high levels of species turnover.     

Lack of adequate taxonomic knowledge may hinder endemic mammal conservation in the Brazilian Atlantic Forest

The Atlantic Forest is one of the most diverse and threatened ecosystems of the world, being thus classified as one of the most important biodiversity hotspots. However, habitat loss, overexploitation, alien species, disease and pollution are not the only threats faced by native fauna and flora. The lack of adequate taxonomic knowledge hinders conservation and management efforts of endemic species. This is true even for mammals, which is the most charismatic group of animals and traditionally receive a good deal of attention from scientists and the public in general. A few examples show how this gap in local fauna information can be demise for species conservation, even misguiding management strategies: molecular data reveal a hidden marsupial diversity; the lack of taxonomic studies at the species level seriously threatens rodent conservation; and the taxonomic rearrangement of the genusBrachyteles revealed a new species and had a great impact on management strategies. New species are discovered, described and taxonomically rearranged at an astounding rate. We can only be successful in biodiversity conservation if we have at least a minimum level of knowledge about what we are trying to preserve. That is true both for researchers and for the general public. Recent taxonomic revisions may represent the turning point in Neotropical fauna knowledge, which, coupled with a greater awareness of local people about the rich biodiversity that dot their backyards, can represent a better conservation prospect for the endemics of the Atlantic Forest.     

Molecular and Morphological Evidence Reveals a New Species in the Phyllomedusa hypochondrialis Group (Hylidae,Phyllomedusinae) from the Atlantic Forest of the Highlands of Southern Brazil

The taxonomic status of a disjunctive population of Phyllomedusa from southern Brazil was diagnosed using molecular, chromosomal, and morphological approaches, which resulted in the recognition of a new species of the P. hypochondrialis group. Here, we describe P. rustica sp. n. from the Atlantic Forest biome, found in natural highland grassland formations on a plateau in the south of Brazil. Phylogenetic inferences placed P. rustica sp. n. in a subclade that includes P. rhodei + all the highland species of the clade. Chromosomal morphology is conservative, supporting the inference of homologies among the karyotypes of the species of this genus. Phyllomedusa rustica is apparently restricted to its type-locality, and we discuss the potential impact on the strategies applied to the conservation of the natural grassland formations found within the Brazilian Atlantic Forest biome in southern Brazil. We suggest that conservation strategies should be modified to guarantee the preservation of this species.