<Emphasis Type="Italic">Isospora lopesi</Emphasis> n. sp. (Apicomplexa: Eimeriidae) from the eastern white-throated spadebill <Emphasis Type="Italic">Platyrinchus mystaceus</Emphasis> Vieillot (Passeriformes: Tyranni: Tyrannidae) in South America

A species of Isospora Schneider, 1881 (Protozoa: Apicomplexa: Eimeriidae) considered as new to science is described and characterised molecularly from the eastern white-throated spadebill Platyrinchus mystaceus Vieillot in the Parque Nacional do Itatiaia, southeastern Brazil. Isospora lopesi n. sp. has oöcysts that are subspheroidal to ovoidal, 18–24 × 18–22 (20.6 × 19.7) µm, with smooth, bilayered wall, c.1.5 μm thick. Micropyle and oöcyst residuum are absent, but one polar granule is present. Sporocysts are ellipsoidal, 12–16 × 8–11 (14.4 × 8.6) µm. The Stieda body is flattened to half-moon-shaped and sub-Stieda body is rounded. Sporocyst residuum is present, consisting of numerous spherules of different sizes. Sporozoites are vermiform with anterior and posterior refractile bodies and nucleus. Molecular analysis was conducted at the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. This new isolate exhibited similarity greater than 98% with Isospora spp. isolates from spectacled warblers Sylvia conspicillata Temminck, 1820. This is the fourth isosporoid coccidian described from New World tyrannid birds, but is the first to have a complementary molecular characterisation.     

Vegetation structure determines insect herbivore diversity in seasonally dry tropical forests

Vegetation structure can often determine insect herbivore fauna in forests, but this mechanism has been demonstrated in seasonally dry tropical forests (SDTFs) only at small spatial scales. In this study we evaluated the effects of the geographical location of SDTFs and vegetation structure on insect herbivore communities (leaf-chewing and sap-sucking guilds) in three Brazilian ecoregions (Cerrado, Cerrado/Caatinga transition, and Caatinga). We tested the following predictions: (1) insect herbivore species composition, richness, abundance and beta diversity differ among forests in different ecoregions; (2) insect richness, abundance and beta diversity are positively related to tree richness and density; (3) spatial turnover of species is the primary mechanism that generates herbivorous insect β-diversity in different ecoregions, and is positively influenced by tree richness. The composition, richness, and abundance of herbivorous insects differed over SDFs along the gradient of Cerrado and Caatinga. Both herbivore guilds responded positively to tree richness. Tree density only determined the richness and abundance of sap-sucking herbivores. Insect β-diversity was similar among Cerrado and transition areas, but lower in Caatinga itself; β-diversity was also positively affected by tree richness. Species turnover, as opposed to nestedness, was the main mechanism generating β-diversity, but itself was not related to tree richness. We demonstrate in this study the importance of landscape diversity and availability of local resources for herbivorous insect communities, and we emphasize the importance of SDTF conservation in different ecoregions as a result of species turnover.     

Food Consumption and Subsistence in Three Caboclo Populations on Marajó Island, Amazonia, Brazil

In this article data on household food consumption is used to further understanding of subsistence strategies in three Caboclo populations on Marajó Island, Amazonia, Brazil. Data were collected using participant observation and 24-hour food recalls in 16 households for 7 consecutive days during the rainy (March) and dry (July) seasons. Marajó-Açu households (n = 6) had the highest levels of energy and protein intake relative to recommendations. This was probably related to their successful integration into the prosperous acai (a palm fruit) market of the riverine area. Praia Grande households (n = 6) had the lowest values for energy intake (rainy season), which supports the authors' ethnographic observations of some instability in the subsistence system of this population. Paricatuba households (n = 4) exhibited intermediate values of energy and protein intakes, but less seasonal variation in consumption than the other two populations. Despite the differences observed, food consumption does not appear to be a major limitation for any of the three populations. The data support recent hypotheses concerning the concomitant and multiple use of várzea (floodplain) and terra firme (upland) environments by the Caboclos and integration into the local market economy as the central strategies in dealing with the so-called socioenvironmental constraints of the Amazonian floodplain.     

Ten simple rules on writing clean and reliable open-source scientific software

Functional, usable, and maintainable open-source software is increasingly essential to scientific research, but there is a large variation in formal training for software development and maintainability. Here, we propose 10 “rules” centered on 2 best practice components: clean code and testing. These 2 areas are relatively straightforward and provide substantial utility relative to the learning investment. Adopting clean code practices helps to standardize and organize software code in order to enhance readability and reduce cognitive load for both the initial developer and subsequent contributors; this allows developers to concentrate on core functionality and reduce errors. Clean coding styles make software code more amenable to testing, including unit tests that work best with modular and consistent software code. Unit tests interrogate specific and isolated coding behavior to reduce coding errors and ensure intended functionality, especially as code increases in complexity; unit tests also implicitly provide example usages of code. Other forms of testing are geared to discover erroneous behavior arising from unexpected inputs or emerging from the interaction of complex codebases. Although conforming to coding styles and designing tests can add time to the software development project in the short term, these foundational tools can help to improve the correctness, quality, usability, and maintainability of open-source scientific software code. They also advance the principal point of scientific research: producing accurate results in a reproducible way. In addition to suggesting several tips for getting started with clean code and testing practices, we recommend numerous tools for the popular open-source scientific software languages Python, R, and Julia.     

Spatial subsidies drive sweet spots of tropical marine biomass production

Spatial subsidies increase local productivity and boost consumer abundance beyond the limits imposed by local resources. In marine ecosystems, deeper water and open ocean subsidies promote animal aggregations and enhance biomass that is critical for human harvesting. However, the scale of this phenomenon in tropical marine systems remains unknown. Here, we integrate a detailed assessment of biomass production in 3 key locations, spanning a major biodiversity and abundance gradient, with an ocean-scale dataset of fish counts to predict the extent and magnitude of plankton subsidies to fishes on coral reefs. We show that planktivorous fish-mediated spatial subsidies are widespread across the Indian and Pacific oceans and drive local spikes in biomass production that can lead to extreme productivity, up to 30 kg ha⁻¹ day⁻¹. Plankton subsidies form the basis of productivity “sweet spots” where planktivores provide more than 50% of the total fish production, more than all other trophic groups combined. These sweet spots operate at regional, site, and smaller local scales. By harvesting oceanic productivity, planktivores bypass spatial constraints imposed by local primary productivity, creating “oases” of tropical fish biomass that are accessible to humans.

How do tropical oceans sustain high productivity and intense coastal fisheries despite occurring in nutrient-poor oceans? This study shows that spatial subsidies dramatically increase local coral reef productivity across the globe, producing localized ‘sweet-spots’ of concentrated, exceptionally high productivity.     

Length–weight relationships for 35 fish species of the Atlantic Forest,SP/RJ—Brazil

Length–weight relationships (LWRs) for 35 freshwater fish species from the SP/RJ coastal basin in Brazil are presented in this paper. Fishes were captured between 2011 and 2015 on an irregular basis using electrofishing, sieves, trawl nets, cast nets and fish‐traps. In this study new LWRs are reported for 28 species, plus the total weight and length for 34 and nine species, respectively. The study provides new information on less‐studied species and can serve as a basis for management and conservation in this area.