Diverse anthropogenic disturbances shift Amazon forests along a structural spectrum.

Amazon forests are being degraded by myriad anthropogenic disturbances, altering ecosystem and climate function. We analyzed the effects of a range of land-use and climate-change disturbances on fine-scale canopy structure using a large database of profiling canopy lidar collected from disturbed and mature Amazon forest plots. At most of the disturbed sites, surveys were conducted 10?30 years after disturbance, with many exhibiting signs of recovery. Structural impacts differed in magnitude more than in character among disturbance types, producing a gradient of impacts. Structural changes were highly coordinated in a manner consistent across disturbance types, indicating commonalities in regeneration pathways. At the most severely affected site ? burned igapó (seasonally flooded forest) ? no signs of canopy regeneration were observed, indicating a sustained alteration of microclimates and consequently greater vulnerability to transitioning to a more open-canopy, savanna-like state. Notably, disturbances rarely shifted forests beyond the natural background of structural variation within mature plots, highlighting the similarities between anthropogenic and natural disturbance regimes, and indicating a degree of resilience among Amazon forests. Studying diverse disturbance types within an integrated analytical framework builds capacity to predict the risk of degradation-driven forest transitions

Amazonia Camtrap: a data set of mammal, bird, and reptile species recorded with camera traps in the Amazon forest.

Abstract : The Amazon forest has the highest biodiversity on Earth. However, information on Amazonian vertebrate diversity is still deficient and scatteredacross the published, peer-reviewed, and gray literature and in unpublishedraw data. Camera traps are an effective non-invasive method of surveying vertebrates, applicable to different scales of time and space. In this study, we organized and standardized camera trap records from different Amazonregions to compile the most extensive data set of inventories of mammal,bird, and reptile species ever assembled for the area. The complete data setcomprises 154,123 records of 317 species (185 birds, 119 mammals, and13 reptiles) gathered from surveys from the Amazonian portion of eightcountries (Brazil, Bolivia, Colombia, Ecuador, French Guiana, Peru,Suriname, and Venezuela). The most frequently recorded species per taxawere: mammals:Cuniculus paca (11,907 records); birds: Pauxi tuberosa (3713 records); and reptiles:Tupinambis teguixin(716 records). The infor-mation detailed in this data paper opens up opportunities for new ecological studies at different spatial and temporal scales, allowing for a moreaccurate evaluation of the effects of habitat loss, fragmentation, climatechange, and other human-mediated defaunation processes in one of themost important and threatened tropical environments in the world. The data set is not copyright restricted; please cite this data paper when usingits data in publications and we also request that researchers and educator sinform us of how they are using these data

Y chromosome sequence and epigenomic reconstruction across human populations

Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications among the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets