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).

Using whole mitochondrial DNA sequences from 89 white-tailed eagles (Haliaeetus albicilla) sampled from Iceland, Greenland, Norway, Denmark and Estonia between 1990-2018, we investigate the mitogenomic variation within and between countries. We show that there is a substantial population differentiation between the countries, reflecting similar major phylogeographic patterns obtained previously for the control region of the mitochondria, which suggested two main refugia during the last glacial period of Ice Age. Distinct mitogenomic lineages are observed within countries which divergence times exceeds the time since last glacial period of Ice Age ended. The lineages appear to have been maintained by natural selection. An excess of segregating amino acids in comparison with number of fixations, as revealed by the neutrality index suggests a load of deleterious mutations. The maintenance of mtDNA lineages within countries inflates our estimates of effective national population sizes and the times of their divergence.

Using whole genome shotgun sequences from 92 white-tailed eagles (Haliaeetus albicilla) sampled from Greenland, Iceland, Norway, Denmark, Estonia, and Turkey between 1885-1950 and after 1990, we investigate the genomic variation within countries over time, and between countries. Clear genetic differentiation is observed between samples from the different countries, with the largest differences between the island and mainland populations, and indications that the island populations share the most recent ancestry with the Norwegian population. We find signs of strong inbreeding in the island populations. Further, temporal differences are observed in some populations, for example, replacement of the Danish gene pool following its population’s extinction in the early 20th century, as well as a change in the genetic diversity of the Icelandic population following a severe bottleneck during the last century, all of which could warrant a further conservation effort in Iceland. More generally, all populations show a decline in effective population size, which may have been shaped by I) distinct refugia during the last glacial period, II) population divergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion and e.g., settlement in Iceland ~1,100 years ago, and IV) human persecution and toxic pollutants during the last two centuries.