Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies

Abstract

<jats:title>Abstract</jats:title> <jats:p>The application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.</jats:p>

Sequence locally, think globally: The Darwin Tree of Life Project

“…We hope and expect that these genomes will then be used by communities of evolutionary, ecological, conservation, and biotechnology scientists to carry out large-scale investigations of species and species groups, and we prioritize species for sequencing based on requests from these groups. From the genomes released already, we are aware of reuse by projects investigating population dynamics in threatened predator species (37), in fish stock monitoring, in lepidopteran speciation dynamics, in ancient environmental DNA analyses, and in large-scale phylogenetics. Additionally, we are developing a rich program of outreach and engagement work bringing DToL to and getting feedback from a wide diversity of stakeholders.…”

Genetic diversity of the endangered Japanese golden eagle at neutral and functional loci

“…Sequences from a Spanish golden eagle (A. c. homeyeri; Alcaide et al, 2007; NCBI accession no. EF370905-EF370908) were used to perform a local BLAST search (BLAST+ version 2.5.0) against the Japanese and Scottish golden eagle genomes (Sato et al, 2020). Upon confirming homology, PCR amplification of the DRB exon 2 region with Acc2FC and Acc2RC was conducted in Japanese golden eagle samples.…”

“…Compared with the vulnerable Galapagos Hawk, which has a similar population size (500-600 individuals, Bollmer et al, 2011), the Japanese golden eagle's diversity indices were significantly higher, suggesting that the Japanese golden eagle's MHC diversity is not critically low, despite their small population size and endangered status. A recent study suggested that Japanese golden eagles likely colonized Japan from both continental Asia and North America during the Last Glacial Period (Sato et al, 2020), which may have contributed to the diverse pool of MHC alleles. Moreover, given that the Japanese golden eagle population is small and isolated, there may be strong tendencies for MHC-based disassortative mating to avoid inbreeding (Potts et al, 1994;e.g., Ryukyu scops owl, Sawada et al, 2020).…”

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

“…The apparent declines, therefore, may not directly relate to immediate conservation problems, but fit within a longer-term pattern of abundance fluctuations. Therefore, there has been an increase in studies incorporating the perspective on longer-term changes in population sizes applied to conservation and management decision-making (Ardren and Kapuscinski, 2003;Brüniche-Olsen et al, 2018;Sato et al, 2020). Genetic techniques provide opportunities to understand historic context of temporal changes at much longer time scales.…”

“…Genetic techniques provide opportunities to understand historic context of temporal changes at much longer time scales. Past population bottlenecks can be detected as well as precipitous declines hundreds and thousands of generations ago (Ramakrishan et al, 2005;Oldeschulte et al, 2017), and currently, assesments of single nucleotide polymorphisms (SNPs) across the entire genome allow exploration of these questions even when very few samples are available (Brüniche-Olsen et al, 2018;Sato et al, 2020). The gray whale (Eschrichtius robustus), for example, already lost its Northern Atlantic populations (probably due to environmental change and/or by commercial whaling), and it is now only found in the Northern Pacific Ocean (Alter et al, 2015).…”