Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community.

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax, and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.

Analysis of the bacterial communities associated with two ant-plant symbioses.

Insect fungiculture is practiced by ants, termites, beetles, and gall midges and it has been suggested to be widespread among plant-ants. Some of the insects engaged in fungiculture, including attine ants and bark beetles, are known to use symbiotic antibiotic-producing actinobacteria to protect themselves and their fungal cultivars against infection. In this study, we analyze the bacterial communities on the cuticles of the plant-ant genera Allomerus and Tetraponera using deep sequencing of 16S rRNA. Allomerus ants cultivate fungus as a building material to strengthen traps for prey, while Tetraponera ants cultivate fungus as a food source. We report that Allomerus and Tetraponera microbiomes contain >75% Proteobacteria and remarkably the bacterial phyla that dominate their cuticular microbiomes are very similar despite their geographic separation (South America and Africa, respectively). Notably, antibiotic-producing actinomycete bacteria represent a tiny fraction of the cuticular microbiomes of both Allomerus and Tetraponera spp. and instead they are dominated by γ-proteobacteria Erwinia and Serratia spp. Both these phyla are known to contain antibiotic-producing species which might therefore play a protective role in these ant-plant systems.

Spatial tools for modeling the sustainability of subsistence hunting in tropical forests.

Subsistence hunting provides a crucial food source for rural populations in tropical forests, but it is often practiced unsustainably. We use the empirical observation that subsistence hunters are central-place foragers to develop three "bio-demographic" hunting models of increasing complexity and realism for assessing the sustainability of hunting of an indicator species. In all our models, we calculate the spatial pattern of depletion of an indicator species (here, a large-bodied primate) across a landscape. Specifically, we show how to identify the area surrounding a human settlement that is expected to suffer local extinction. Our approach is an improvement over well-known sustainability indices of hunting, which are prone to error and do not provide clear links to policy prescriptions. Our first approach models the long-term effect of a single settlement and (1) can be parameterized with easily obtainable field data (such as settlement maps and knowledge of the major weapon used), (2) is simple enough to be used without requiring technical skill, and (3) reveals the asymptotic relationship between local human density and the level of game depletion. Our second model allows multiple settlements with overlapping hunting zones over large spatial scales. Our third model additionally allows temporal changes in human population size and distribution and source-sink dynamics in game populations. Using transect and hunting data from two Amazonian sites, we show that the models accurately predict the spatial distribution of primate depletion. To make these methods accessible, we provide software-based tools, including a toolbox for ArcGIS, to assist in managing and mapping the spatial extent of hunting. The proposed application of our models is to allow the quantitative assessment of settlement stabilization approaches to managing hunting in Amazonia.

The market triumph of ecotourism: an economic investigation of the private and social benefits of competing land uses in the Peruvian Amazon.

Annual revenue flow to developing countries for ecotourism (or nature-based tourism) could be as large as US$ 210×10(12), providing an enormous financial incentive against habitat loss and exploitation. However, is ecotourism the most privately and/or socially valuable use of rainforest land? The question is rarely answered because the relevant data, estimates of profits and fixed costs, are rarely available. We present a social cost-benefit analysis of land use in an ecotourism cluster in the Tambopata region of Amazonian Peru. The net present value of ecotourism-controlled land is given by the producer surplus (profits plus fixed costs of ecotourism lodges): US$ 1,158 ha(-1), which is higher than all currently practiced alternatives, including unsustainable logging, ranching, and agriculture. To our knowledge, this is the first sector-wide study of profitability and producer surplus in a developing-country ecotourism sector and the first to compare against equivalent measures for a spectrum of alternative uses. We also find that ecotourism-controlled land sequesters between 5.3 to 8.7 million tons of above-ground carbon, which is equivalent to between 3000-5000 years of carbon emissions from the domestic component of air and surface travel between the gateway city of Cusco and the lodges, at 2005 emission rates. Ecotourism in Tambopata has successfully monetized the hedonic value of wild nature in Amazonian Peru, and justifies the maintenance of intact rainforest over all alternative uses on narrow economic grounds alone.

The evolution of intermediate castration virulence and ant coexistence in a spatially structured environment.

Theory suggests that spatial structuring should select for intermediate levels of virulence in parasites, but empirical tests are rare and have never been conducted with castration (sterilizing) parasites. To test this theory in a natural landscape, we construct a spatially explicit model of the symbiosis between the ant-plant Cordia nodosa and its two, protecting ant symbionts, Allomerus and Azteca. Allomerus is also a castration parasite, preventing fruiting to increase colony fecundity. Limiting the dispersal of Allomerus and host plant selects for intermediate castration virulence. Increasing the frequency of the mutualist, Azteca, selects for higher castration virulence in Allomerus, because seeds from Azteca-inhabited plants are a public good that Allomerus exploits. These results are consistent with field observations and, to our knowledge, provide the first empirical evidence supporting the hypothesis that spatial structure can reduce castration virulence and the first such evidence in a natural landscape for either mortality or castration virulence.

The sustainability of subsistence hunting by Matsigenka native communities in Manu National Park, Peru.

The presence of indigenous people in tropical parks has fueled a debate over whether people in parks are conservation allies or direct threats to biodiversity. A well-known example is the Matsigenka (or Machiguenga) population residing in Manu National Park in Peruvian Amazonia. Because the exploitation of wild meat (or bushmeat), especially large vertebrates, represents the most significant internal threat to biodiversity in Manu, we analyzed 1 year of participatory monitoring of game offtake in two Matsigenka native communities within Manu Park (102,397 consumer days and 2,089 prey items). We used the Robinson and Redford (1991) index to identify five prey species hunted at or above maximum sustainable yield within the approximately 150-km(2) core hunting zones of the two communities: woolly monkey (Lagothrix lagotricha), spider monkey (Ateles chamek), white-lipped peccary (Tayassu pecari), Razor-billed Currasow (Mitu tuberosa), and Spix's Guan (Penelope jacquacu). There was little or no evidence that any of these five species has become depleted, other than locally, despite a near doubling of the human population since 1988. Hunter-prey profiles have not changed since 1988, and there has been little change in per capita consumption rates or mean prey weights. The current offtake by the Matsigenka appears to be sustainable, apparently due to source-sink dynamics. Source-sink dynamics imply that even with continued human population growth within a settlement, offtake for each hunted species will eventually reach an asymptote. Thus, stabilizing the Matsigenka population around existing settlements should be a primary policy goal for Manu Park.

Demographic threats to the sustainability of Brazil nut exploitation.

A comparative analysis of 23 populations of the Brazil nut tree (Bertholletia excelsa) across the Brazilian, Peruvian, and Bolivian Amazon shows that the history and intensity of Brazil nut exploitation are major determinants of population size structure. Populations subjected to persistent levels of harvest lack juvenile trees less than 60 centimeters in diameter at breast height; only populations with a history of either light or recent exploitation contain large numbers of juvenile trees. A harvesting model confirms that intensive exploitation levels over the past century are such that juvenile recruitment is insufficient to maintain populations over the long term. Without management, intensively harvested populations will succumb to a process of senescence and demographic collapse, threatening this cornerstone of the Amazonian extractive economy.