Data S1: Illegal activities dataset

Background The Brazilian Amazon is the world’s largest rainforest regions and plays a key role in biodiversity conservation as well as climate adaptation and mitigation. The government has created a network of protected areas (PAs) to ensure long-term conservation of the region. However, despite the importance of and positive advances in the establishment of PAs, natural resource depletion in the Brazilian Amazon is pervasive. Methods We evaluated a total of 4,243 official law enforcement records generated between 2010 and 2015 to understand the geographical distribution of the illegal use of resources in federal PAs in the Brazilian Amazon. We classified illegal activities into ten categories and used generalized additive models (GAMs) to evaluate the relationship between illegal use of natural resources inside PAs with management type, age of PAs, population density, and accessibility. Results We found 27 types of illegal use of natural resources that were grouped into 10 categories of illegal activities. Most infractions were related to suppression and degradation of vegetation (37.40%), followed by illegal fishing (27.30%) and hunting activities (18.20%). The explanatory power of the GAMs was low for all categories of illegal activity, with a maximum explained variation of 41.2% for illegal activities as a whole, and a minimum of 14.6% for hunting activities. Discussion These findings demonstrate that even though PAs are fundamental for nature conservation in the Brazilian Amazon, the pressures and threats posed by human activities include a broad range of illegal uses of natural resources. Population density up to 50 km from a PA is a key variable, influencing illegal activities. These threats endanger long-term conservation and many efforts are still needed to maintain PAs that are large enough and sufficiently intact to maintain ecosystem functions and protect biodiversity

Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish

Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species- specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps and geological faults. The morphological (colour pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within river systems and, consequently, the dynamics of gene flow between freshwater lineages/species.River networks are spatially and temporally dynamic environments that impose challenges to the study of hybrid zones. Here, we elucidate the morphological and genetic structure of a hybrid zone generated by secondary contact between lineages of a Neotropical fish genus and discuss the possible role of past and current river properties (including river captures) in its origin and structure.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163541/3/jeb13689_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163541/2/jeb13689-sup-0001-AppendixS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163541/1/jeb13689.pd