Abstract

Abstract

Abstract

Abstract
The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint.

Abstract

Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was nonsignificant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.