A taxonomic account of Myrcia (Myrtaceae) at the sites of the Biological Dynamics of Forest Fragments Project, Amazonas, Brazil

Myrcia is the sole genus of the Myrciinae, one of the nine subtribes of Myrteae (Myrtaceae). The Amazon forest holds about one-quarter of the Brazilian species of Myrcia, but the genus is still understudied in this whole region. In this context, this study presents a floristic survey of Myrcia in the permanent plots of the Biological Dynamics of Forest Fragments Project (BDFFP), in Amazonas state, Brazil. The genus is represented by 36 species in the study area, comprehending 32% of its total richness in the Brazilian Amazon forest, with 19 of them endemic to this domain. Myrcia neospeciosa is reported as a new occurrence for Amazonas state and M. grandis is recorded for the first time from upland terra firme forests on clayish soils. Myrcia cuspidata, a species with calyptrate flowers, is classified under Myrcia sect. Aulomyrcia, representing the second taxon of the genus with this feature removed from Myrcia sect. Calyptranthes. Finally, morphological aspects of the infra-generic categories of Myrcia are reported more overlapping than previously thought. A map containing the location of the study area, an identification key, descriptions, comments, and figures are provided.

BD5: an open HDF5-based data format to represent quantitative biological dynamics data

BD5 is a new binary data format based on HDF5 (hierarchical data format version 5). It can be used for representing quantitative biological dynamics data obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) is an XML(Extensible Markup Language)-based open format that is also used to represent such data; however, it becomes difficult to access quantitative data in BDML files when the file size is large because parsing XML- based files requires large computational resources to first read the whole file sequentially into computer memory. BD5 enables fast random (i.e., direct) access to quantitative data on disk without parsing the entire file. Therefore, it allows practical reuse of data for understanding biological mechanisms underlying the dynamics.

Birds in fragmented Amazonian rainforest: Lessons from 40 years at the Biological Dynamics of Forest Fragments Project

For decades, ecologists have studied fundamental questions of how Amazonian biodiversity is maintained, and whether that diversity can persist following deforestation. The long history of avian research at the Biological Dynamics of Forest Fragments Project, near Manaus, Brazil, has helped advance this understanding in the context of a broader research program focused on rainforest fragments embedded in a dynamic matrix. By sampling birds beginning before fragments were isolated, in the late 1970s, and continuing the protocol to the present, our work has revealed community dynamics driven not just by area and isolation, but also by larger landscape patterns, particularly second growth recovery over decadal scales. Fragments permanently lose some bird species, but their communities need not follow a trajectory toward catastrophic change. Our challenge now is to determine under what conditions remnant patches and developing second growth can support not just the rich diversity of Amazonian rainforest species but also their population processes and emergent community properties.