Unexpected hybridisation and limited population structure uncovers perplexing taxonomic issues in the Australian, Little, and Forest Ravens

Hybridisation is common across the tree of life, and signals of introgression can be found in the genomes of birds worldwide. However, it is not always easy to differentiate between alternative evolutionary histories from genomic data. Here we use reduced representation sequencing to test hypotheses concerning the taxonomy and evolutionary history of a recently diverged lineage endemic to Australia containing three species – the Australian Raven (Corvus coronoides), Little Raven (C. mellori) and Forest Raven (C. tasmanicus) Raven. Similar flocking behaviour, morphometrics, plumage and vocalisations might suggest that the western subspecies of the Australian Raven C. c. perplexus is sister to C. mellori. Our data reject that hypothesis, instead, we find clear support for current species boundaries. Unexpectedly, however, we find genomic evidence for hybridisation between C. mellori and C. coronoides in south-eastern Australia. Whether subspecies are warranted within C. coronoides depends on the resolution of the significance of two critical sampling gaps and whether isolation-by-distance or historical allopatry and secondary contact best explain population structure. Vicariance, isolation-by-distance, hybridisation and introgression all need careful consideration in widespread Australian birds. We highlight identification challenges among phenotypically similar species that also hybridise and the critical evolutionary insights that can be gained from historical museum specimens.