Abstract

BackgroundDarwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored.ResultsWe characterized the microbial community associated with 12 species of Darwin’s finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin’s finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception—the vampire finch—which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia—bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ15N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons.ConclusionsThis study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.

Highlights

  • Darwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a classic example of adaptive radiation

  • The core gut microbiome of Darwin’s finches The 16S rRNA gene diversity of the gut microbiome of Darwin’s finches was characterized from fecal samples collected from 114 finches, representing 12 of 19 species distributed across nine of the Galápagos Islands (Fig. 1; Table 1; note that as a singleton, sequence data from the one specimen of C. pallida was removed from subsequent analysis)

  • This dataset yielded an average of 25,382 16S rRNA sequences per finch and collectively comprised 297 unique bacterial ribotypes (OTUs; 97% similarity level), present above a minimum threshold set at 1% relative abundance in at least one finch in the dataset

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Summary

Introduction

Darwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored. Diet has long been recognized as a major factor in the adaptive radiation of Michel et al Microbiome (2018) 6:167 finches in the Galápagos, as lineages on different islands developed beaks specialized for food sources available on their islands, with selective pressure especially high during the dry season when food sources are most limited [10]. Studies have focused on clades that diverged tens of millions of years ago, whereas less is known about the degree of gut microbiome divergence in younger, relatively recent species radiations

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