Phylogeny, population structure, and conservation genomics of Galapagos vermilion flycatchers (genus Pyrocephalus)

The Galapagos archipelago in the Eastern Tropical Pacific is known for its isolation, island endemism, and rapid diversification. Despite considerable scientific research many groups remain poorly studied. One of these groups is the genus Pyrocephalus, a group of brightly-colored and charismatic flycatchers whose populations have declined significantly in recent decades. To study the evolution and diversification of Pyrocephalus, we used samples from 53 individuals across 11 Galapagos Islands (Pyrocephalus dubius and P. nanus) and a continental outgroup (P. obscurus) and reconstructed a phylogeny using 233,916 genome-wide SNPs. The data revealed that Pyrocephalus colonized Galapagos earlier than previously estimated, approximately 1.3 million years ago (MYA), and diversified into at least eight genetically distinct clades. These include P. dubius, a species endemic to San Cristobal Island, now extinct, and P. nanus across the remaining islands. The P. nanus population on Floreana Island has been isolated for at least 1.2 MYA, along with additional divergent groups from Santa Cruz, Pinzon + Rabida, Isabela + Fernandina, Santiago, Marchena and Pinta, which have each been isolated for 0.89-0.15 million years. Morphometric, plumage and acoustic comparisons corroborate many of these genetic clades. Specifically for Santa Cruz Island, population genetic analyses indicate a significant reduction in nucleotide diversity, but no evidence of inbreeding, suggesting a minimal recent migration and rapid population decline. Our data on genetic diversification are critical for identifying evolutionary distinct populations and guiding translocations to restore extirpated or diminished island populations.