Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics

Abstract

The taxonomic classification of a falcon population found in the Altai region in Asia has been heavily debated for two centuries and previous studies have been inconclusive, hindering a more informed conservation approach. Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 44 falcons from different species and populations, including "Altai" falcons, we analyzed their population structure, admixture patterns and demographic history. We find that the Altai falcons are genomically mosaic of saker and gyrfalcon ancestries, and carry distinct W- and mitochondrial-haplotypes that cluster with the lanner falcon. The Altai haplotype diverged 422,000 years ago from the ancestor of sakers and gyrfalcons, both of which, in turn, split 109,000 years ago. The Altai W chromosome includes coding variants that may influence important structural, behavioral and reproductive traits. These findings support the designation of Altai falcons as a distinct falcon species (Falco altaicus).

Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus)

“…This would also explain the significant admixture found in our study (Fig. 9 ) and repeatedly reported by others 30 , 31 . Nonetheless, this interpretation does not affect the significance of pre-adapted genetic parts reported by Hu et al in the successful colonization of the Qinghai–Tibet Plateau by ancestral western Mongolian sakers.…”

“…This landscape south of the permafrost zone must have also been rich in rodents and could have been the ancient habitat of the saker. This could be the period when the species expanded its distribution range the most, as supported by effective population size reconstructions 29 – 31 . This large range became fragmented most likely in the Holocene, similar to that of the peregrine falcon ( F. peregrinus ) 47 .…”

“…In contrast, WGS data suggests an older split ( ca 300 kyr) of ancestral sakers from gyrfalcons, yet, this is not supported by our findings. A third stem age of sakers was estimated by Al-Ajli et al 31 who report the separation at 109 kyr ago. Given this uncertainty in saker stem age, we cannot set the exact timing of evolutionary events, but hypothesize below the possible evolutionary history based on our results.…”

“…In this respect it is especially relevant to refer to two recent papers 30 , 31 utilizing a genomic approach on the origin of eastern sakers which were published during the review process of our work. Hu et al 30 accepted the general view on gyrfalcons being the sister species of (a monophyletic eastern and western) saker, and thus used the former as outgroup in their analyses.…”

“…In more recent work based on whole-genome resequencing, Hu et al 30 reinterpreted previous results and assessed the separation of gyrfalcons and sakers to much earlier, ca 300 kyr ago, and the subsequent expansion of sakers from Europe to Asia at 41 (38–78) kyr ago. Morover, a recently published study 31 set the divergence between the above-mentioned species at ca 109 kyr ago.…”