Whole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes and, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types can have highly disparate evolutionary histories, it is imperative to take this information into account when analyzing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome using two whole genome sequenced (WGS) and 133 RAD sequenced white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold, ii) heterozygosity per scaffold in a male and female bird, iii) mapping to a reference genome of a related species (chicken) with identified sex chromosomes, and iv) an analysis of SNP-loadings from a principal components analysis (PCA), based on low-depth RADseq data from 133 individuals. In i and ii, the WGS were mapped to a reference genome consisting of 1142 assembled scaffolds from the golden eagle (Aquila chrysaetos) with no identified chromosomes. The read depth per scaffold identified 86.41% of the homogametic sex chromosome (Z) with few false positives. The SNP-loading scores found 78.6% of the Z-chromosome but had a false positive discovery rate of more than 10%. The heterozygosity per scaffold did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W).

Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities. As such, it has high potential utility for routine environmental assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected along an organic enrichment gradient at six salmon farms in British Columbia, Canada, and benthic biotic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analyzing 11,466 individuals using a combination of morpho-taxonomy and DNA barcoding. Study objectives were to: (1) compare biotic signals associated with benthic impacts of salmon farming in the two data types; and (2) identify potential eDNA indicators to facilitate eDNA-based monitoring in Canada. Across both data types, alpha diversity parameters were reduced in sediments near fish cage edge and were negatively correlated with pore-water sulphide concentration. Presence/absence of known indicator taxon Capitella generally agreed well between the two methods despite that they differed in both the volume of sediment sampled and the molecular marker used. In eDNA data, there was a strong negative correlation between Nematoda OTU richness and pore-water sulphide concentration, and multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop a local biotic index.