The Burrowing Parrot, Cyanoliseus patagonus, is no ordinary bird. It breeds in colonies dug into soft sandstone and limestone cliffs known as barrancas, and the colony near El Cóndor, beside the Río Negro estuary, is the largest known colony of any parrot species on Earth. Stretching 18.1 kilometers along the coast, it holds roughly 71 percent of the global breeding population, with long-term monitoring between 1998 and 2019 recording between 22,000 and 41,000 active nests. Understanding what these birds eat is therefore not a niche question of natural history; it is central to the survival of the majority of the species.

Historically, Burrowing Parrots were thought to feed mainly on the native vegetation of the Monte and Espinal ecoregions: seeds and fruits of chañar, caldén, algarrobo trees, berries of native shrubs such as Lycium, Discaria and Schinus, and grasses of the arid scrubland. Early naturalists, including W. H. Hudson in 1923 and Alexander Wetmore in 1926, described a diet rooted firmly in Patagonia’s native flora. The new study, published in The Science of Nature, tells a very different story. Of 202 valid plant molecular operational taxonomic units, or MOTUs, identified in the parrots’ droppings over the annual cycle, only 13 percent corresponded to native plants. Fully 40 percent were introduced species, with a further 4.5 percent presumed introduced, 12 percent ornamental garden plants, and 6.9 percent cultivated crops and pastures.

The methodology behind these numbers is a textbook example of modern molecular scatology. Between January and December 2021, the researchers collected 220 fresh fecal samples from the roosting flocks — 20 per month, except February, when the parrots mysteriously abandon the village roost. DNA was extracted from 178 samples using a stool kit optimized with bead-beating homogenization and extended incubation. Two primer sets were then amplified: one targeting the second internal transcribed spacer (ITS2) of plant nuclear ribosomal DNA, and a second targeting Bilateralia, the group that includes all animals with bilateral symmetry, to detect parasites and other animal DNA. The libraries were sequenced on an Illumina MiSeq with 250-base-pair paired-end reads.

The bioinformatic pipeline was equally rigorous. Reads were quality-trimmed with TRIMMOMATIC, merged with FLASH, de-replicated and screened for chimeras with USEARCH, and clustered into MOTUs. Each MOTU was then matched against the NCBI GenBank nucleotide database using BLASTn, with stringent thresholds: sequences had to be at least 190 base pairs long, with matches above 98 percent identity and an e-value below 0.00001. Species-level assignments required matches above 99.5 percent with consistent quality metrics across all retained hits. Negative extraction controls and PCR-grade water controls showed no contamination, and a dedicated gap analysis confirmed that the reference libraries were adequate: 69 percent of native plant species in the region have reference sequences in GenBank, rising to 97 percent at the genus level — sufficient given that 85 percent of the recovered MOTUs could be assigned to genus or better.

The seasonal patterns that emerged were striking. The parrots consumed 77 plant taxa during the breeding season, 172 during the post-breeding period, 72 in winter and 70 during pre-breeding — a statistically significant difference, with dietary diversity peaking just after the chicks fledge. This post-breeding explosion in dietary breadth coincides with the period when most plants in the region produce fruits and release seeds, and it is a critical window for juvenile survival, as young parrots must build up reserves before the harsh Patagonian winter. Non-metric multidimensional scaling and permutational multivariate analysis of variance revealed considerable overlap in diet across breeding, post-breeding and pre-breeding stages, but far less overlap with winter, when the birds turn to plants such as white spruce, velvet grass, perennial ryegrass and other introduced and ornamental species that are absent from the diet at other times of year.

Could the dominance of introduced plants be an artifact of sampling location? The researchers considered this carefully. Because samples were collected in the evening at the village roost, the diet might theoretically be biased toward items eaten near El Cóndor, where the landscape is most heavily modified. But several lines of evidence argue against it. Observations over five breeding seasons show the parrots flying over fields near the village without stopping to feed, and previous tracking studies show they forage between 58 kilometers northwest and 66 kilometers northeast of the colony. Moreover, digestive transit studies in parrots — corn-fed budgerigars empty their entire digestive tract within 26 hours — indicate that the DNA detected in evening droppings most likely reflects a full day of foraging, not just the last hours.

The most plausible explanation, the authors argue, is environmental degradation. Since the 1970s, a combination of increased rainfall and aggressive land clearing has transformed the region. In the Patagones department, natural vegetation that covered 65 percent of the land in 1975 has been reduced to an estimated 20 to 29 percent; in just three years, from 2015 to 2018, more than 216,000 hectares were cleared. In Adolfo Alsina department, home to El Cóndor, nearly 49,000 hectares were cleared between 1986 and 2006. Such landscape-scale disturbance disrupts native plant communities and opens the door to alien species. The parrots, it appears, are switching from a diet historically based on Monte and Espinal plants to one now dominated by introduced species — either a remarkable display of behavioral flexibility, or a warning sign of a suboptimal strategy that could undermine the persistence of the world’s largest parrot colony. A persistent La Niña event before and during the study may also have reduced the availability of native plants, though the authors caution that a single year of sampling cannot establish causation, and multi-year research is essential, especially as La Niña events are expected to become more frequent under climate change.

The study also delivered an unexpected bonus: a parasitological survey conducted entirely from droppings. Using the Bilateralia primer, the team identified 31 animal MOTUs, including four parasite families never before recorded in the digestive tracts of Burrowing Parrots: Gongylonematidae, which infects the oral cavity of birds and can cause starvation and death; Hymenolepididae and Onchobothriidae, both tapeworm groups previously unknown in parrots — Onchobothriidae had never been reported in any bird; and Capillariidae, thin nematodes known from captive parrots. The Gongylonematidae finding is particularly intriguing. During the 2020–2021 breeding season, at least 1,050 adult parrots died at El Cóndor — compared with the 20 to 30 typically found dead each year — and veterinary experts suspected infection rather than starvation as the primary cause. The authors stress that they can only speculate about a connection, but the possibility of a widespread Gongylonematidae infection driving that mortality event now demands investigation.

For decades, Burrowing Parrots were persecuted as agricultural pests, blamed for damage to maize, sunflowers, wheat and fruit orchards. The evidence tells a more nuanced story: systematic evaluations found that the birds affected only 0.1 to 0.4 percent of the sunflower harvest, leaving wheat and maize undamaged, and the species has been removed from Argentina’s pest-control lists. The new data reinforce this picture — cultivated plants made up just 6.9 percent of the diet, and official agricultural statistics suggest these mostly correspond to forage pastures of oats and barley rather than standing crops. As the clearance of the Monte continues and the El Cóndor colony concentrates the vast majority of the world’s Burrowing Parrots, the authors call for close monitoring of both population size and diet. The droppings collected under those Patagonian power lines have done more than reveal a menu; they have documented a dietary revolution in real time, flagged nine plant species newly introduced to the region, and possibly left a molecular clue to a mass mortality that still awaits explanation.

Subject of Research: Seasonal diet composition of Burrowing Parrots revealed by DNA metabarcoding of fecal samples

Article Title: Using next-generation sequencing to unravel the diet composition of Burrowing Parrots over the annual cycle

Article References: Masello, J. F., Failla, M., Leder, C. V., & Quillfeldt, P. (2026). Using next-generation sequencing to unravel the diet composition of Burrowing Parrots over the annual cycle. The Science of Nature, 113(5), Article 119. https://doi.org/10.1007/s00114-026-02159-3

Image Credits: AI Generated

DOI: 10.1007/s00114-026-02159-3

Keywords: Burrowing Parrot, DNA metabarcoding, next-generation sequencing, diet composition, Patagonia, El Cóndor colony, molecular scatology, introduced plants, environmental degradation, parasites, Psittaciformes, La Niña