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.

Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: I) isolation of refugia during the last glacial period 110-115,000 years ago, II) population divergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion, which led to the settlement in Iceland ~1,100 years ago, and IV) human persecution and exposure to toxic pollutants during the last two centuries.

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.