Scientific research increasingly calls for open‐source software that is flexible, interactive, and expandable, while providing methodological guidance and reproducibility. Currently, many analyses in ecology are implemented with “black box” graphical user interfaces (GUIs) that lack flexibility or command‐line interfaces that are infrequently used by non‐specialists. To help remedy this situation in the context of species distribution modeling, we created Wallace, an open and modular application with a richly documented GUI with underlying R scripts that is flexible and highly interactive. Wallace guides users from acquiring and processing data to building models and examining predictions. Additionally, it is designed to grow via community contributions of new modules to expand functionality. All results are downloadable, along with code to reproduce the analysis. Wallace provides an example of an innovative platform to increase access to cutting‐edge methods and encourage plurality in science and collaboration in software development.

Protected areas in Brazil are effective in reducing loss of natural vegetation, especially in Amazon and indigenous lands.

The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species.