Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories

Integrating eDNA metabarcoding and citizen science enhances avian ecological research

Research Highlight: Bourbour et al., 2024. Feeding en route: Prey availability and traits influence prey selection by an avian predator on migration. Journal of Animal Ecology. Diet selection plays a key role in the eco-evolutionary dynamics of animals, exhibiting substantial variability across species, environments and seasons. The complex interplay between movement capability, hunting strategies, habitat use, prey traits and availability shapes the foraging patterns of avian predators. However, detailed information on how these birds exploit their extensive territories remains limited. In this study, Bourbour et al. utilised a novel integration of eDNA metabarcoding and citizen science to explore predator-prey interactions between migrating sharp-shinned hawks (Accipiter striatus) and an ephemeral avian prey community along North America's Pacific flyway. The research identified 1396 detections from the diet (65 species) of 588 migrating sharp-shinned hawks. Hawks' diet composition correlated with prey abundance indices sourced from the eBird database throughout the migration season, highlighting the significant impact of prey availability-shaped by migration tendency, flocking behaviour, and habitat-on raptor-songbird interactions. Notably, the study also found significant differences in prey size between male and female hawks, indicating that sexual dimorphism has led to diverse foraging strategies during migration. These findings underscore the potential of combining eDNA metabarcoding with citizen science to deepen our understanding of the foraging ecology of highly mobile and wide-ranging birds, as well as to monitor complex and vast ecosystems.

Millennia-old coral holobiont DNA provides insight into future adaptive trajectories

Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.

Mitogenomic analysis of extant condor species provides insight into the molecular evolution of vultures

The evolution of large vultures linked to mountainous habitats was accompanied by extreme physiological and behavioral specializations for energetically efficient flights. However, little is known on the genetic traits associated with the evolution of these obligate soaring scavengers. Mitochondrial DNA plays a vital role in regulating oxidative stress and energy production, and hence may be an important target of selection for flight performance. Herein, we characterized the first mitogenomes of the Andean and California condors, the world's heaviest flying birds and the only living representatives of the Vultur and Gymnogyps genus. We reconstructed the phylogenetic relationships and evaluated possible footprints of convergent evolution associated to the life-history traits and distributional range of vultures. Our phylogenomic analyses supported the independent evolution of vultures, with the origin of Cathartidae in the early Paleogene (~ 61 Mya), and estimated the radiation of extant condors during the late Miocene (~ 11 Mya). Selection analyses indicated that vultures exhibit signals of relaxation of purifying selection relative to other accipitrimorph raptors, possibly indicating the degeneration of flapping flight ability. Overall, our results suggest that the extreme specialization of vultures for efficient soaring flight has compensated the evolution of large body sizes mitigating the selection pressure on mtDNA.

Genome-wide diversity in the California condor tracks its prehistoric abundance and decline

Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.¹ During the latter half of the twentieth century, North America's largest soaring bird,² the California condor (Gymnogyps californianus; Critically Endangered³), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor's recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,⁴ but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable³) and the turkey vulture (Cathartes aura; Least Concern³). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.