Ancient genomics reveals lost giant chaffinch ecomorphs in the Azores

<title>Abstract</title> <p> <bold>Background</bold> Islands harbour exceptional concentrations of endemic biodiversity, yet their biotas have been profoundly reshaped by human colonisation. In the Azores, deforestation and the introduction of invasive mammals drove major ecological transformations, and the fossil record reveals that the archipelago once supported avian communities far more diverse than those of today. During palaeontological expeditions conducted between 2011 and 2018, we recovered cranial and postcranial remains from several islands that were unambiguously assigned to the genus <italic>Fringilla</italic> , but exhibited substantially enlarged cranial morphology relative to the extant Azorean common chaffinch ( <italic>F. moreletti</italic> ). Remarkably, skull and beak proportions closely resembled those of the Canary Islands blue chaffinches ( <italic>F. teydea</italic> and <italic>F. polatzeki</italic> ), raising the possibility of a shared evolutionary origin. <bold>Results</bold> Using endogenous DNA extracted from fossil remains, we reconstructed complete or near-complete mitochondrial genomes from seven individuals. Combined with dense taxonomic sampling and whole-genome resequencing across <italic>Fringilla</italic> , these data enabled reconstruction of the evolutionary history of the Azorean forms. Contrary to expectations based on morphology, phylogenetic analyses unequivocally placed the extinct giant morphotypes within the clade of extant Azorean common chaffinches. <bold>Conclusions</bold> These findings reveal an extraordinary degree of ecological plasticity in passerines and demonstrate that pronounced morphological divergence can evolve without substantial genome-wide divergence. More broadly, our results highlight the importance of integrating genomic and morphological evidence when reconstructing the evolutionary history of extinct island taxa. </p>