Habitat restoration to conserve the Little Vermilion Flycatcher on Santa Cruz Island, Galapagos.

The endemic Little Vermilion Flycatcher (LVF), Pyrocephalus nanus, has suffered a drastic decline on Santa Cruz Island, where it was common 30 years ago. Currently, less than 40 individuals remain in the last remnants of natural humid forest in the Galapagos National Park on this island. This small population has low reproductive success, which is contributing to its decline in Santa Cruz. Previous studies have identified Avian Vampire Fly, Philornis downsi, parasitism, changes in food sources, and habitat alteration as threats to this species. In Santa Cruz, invasive plants may strongly affect the reproductive success of the LVF because they limit accessibility to prey near the ground, the preferred foraging niche of these birds. Since 2019, we restored the vegetation in seven plots of one hectare each by removing invasive blackberry plants and other introduced plant species. In all nests that reached late incubation, we also reduced the number of Avian Vampire Fly larvae. In this study, we compared foraging and perch height, pair formation, incubation time and reproductive success between managed and unmanaged areas. As predicted, we found significantly lower foraging height and perch height in 2021 in managed areas compared to unmanaged areas. In 2020, daily failure rate (DFR) of nests in the egg stage did not differ between management types; however, in 2021, DFR in the egg stage was significantly lower in managed areas than in unmanaged areas. The DFR during the nestling stage was similar between managed and unmanaged areas in 2020, but in 2021, only nests in managed areas reached the nestling stage. Females brooded significantly more during the incubation phase in managed areas. Additionally, we found significantly higher reproductive success in managed areas compared to unmanaged areas in 2021, but not in 2020. Habitat restoration is a long-term process and these findings suggest that habitat management positively affects this small population in the long term.

Genome Assembly of Pyrocephalus nanus: A Step Toward the Genetic Conservation of the Endangered Little Vermilion Flycatcher of the Galapagos Islands.

Incredibly powerful whole genome studies of conservation genetics, evolution, and biogeography become possible for non-model organisms when reference genomes are available. Here, we report the sequence and assembly of the whole genome of the little vermilion flycatcher (Pyrocephalus nanus; family Tyrannidae), which is an endemic, endangered, and declining species of the Galapagos Islands. Using PacBio HiFi reads to assemble long contigs and Hi-C reads for scaffolding, we assembled a genome of 1.07 Gb comprising 267 contigs in 152 scaffolds, scaffold N50 74 M, contig N50 17.8 M, with 98.9% assigned to candidate chromosomal sequences and 99.72% of the BUSCO passeriformes 10,844 single-copy orthologs present. In addition, we used the novel HiFiMiTie pipeline to fully assemble and verify all portions of the mitochondrial genome from HiFi reads, obtaining a mitogenome of 17,151 bases, containing 13 protein-coding genes, 22 tRNAs, 2 rRNAs, two control regions, and a unique structure of control region duplication and repeats. These genomes will be a critical tool for much-needed studies of phylogenetics, population genetics, biogeography, and conservation genetics of Pyrocephalus and related genera. This genome and other studies that use it will be able to provide recommendations for conservation management, taxonomic improvement, and to understand the evolution and diversification of this genus within the Galapagos Islands.