Contamination is a ubiquitous problem in microbiome research and can skew results, especially when small amounts of target DNA are available. Nevertheless, no clear solution has emerged for removing microbial contamination. To address this problem, we developed the R package microDecon (https://github.com/donaldtmcknight/microDecon), which uses the proportions of contaminant operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) in blank samples to systematically identify and remove contaminant reads from metabarcoding data sets. We rigorously tested microDecon using a series of computer simulations and a sequencing experiment. We also compared it to the common practice of simply removing all contaminant OTUs/ASVs and other methods for removing contamination. Both the computer simulations and our sequencing data confirmed the utility of microDecon. In our largest simulation (100,000 samples), using microDecon improved the results in 98.1% of samples. Additionally, in the sequencing data and in simulations involving groups, it enabled accurate clustering of groups as well as the detection of previously obscured patterns. It also produced more accurate results than the existing methods for identifying and removing contamination. These results demonstrate that microDecon effectively removes contamination across a broad range of situations. It should, therefore, be widely applicable to microbiome studies, as well as to metabarcoding studies in general.

During a biological invasion, we expect that the expanding front will increasingly become dominated by individuals with better dispersal abilities. Over many generations, selection at the invasion front thus will favour traits that increase dispersal rates. As a result of this process, cane toads (Bufo marinus) are now spreading through tropical Australia about 5-fold faster than in the early years of toad invasion; but how have toads changed to make this happen? Here we present data from radio-tracking of free-ranging cane toads from three populations (spanning a 15-year period of the toads’ Australian invasion, and across 1800 km). Our data reveal dramatic shifts in behavioural traits (proportion of nights when toads move from their existing retreat-site to a new one, and distance between those successive retreat-sites) associated with the rapid acceleration of toad invasion. Over a maximum period of 70 years (~50 generations), cane toads at the invasion front in Australia apparently have evolved such that populations include a higher proportion of individuals that make long, straight moves.