Genomics is an invaluable tool for conservation, particularly for endangered species impacted by wildlife trafficking. This study uses genomic data to provide new insights to aid conservation and management of endangered species, using as a case study the Yellow cardinal (Gubernatrix cristata), a bird endemic to southern South America severely affected by illegal trade and the transformation of its natural habitat. We explore population structure within the Yellow cardinal, delimiting management units and describing connectivity among them. Additionally, we develop and assess the accuracy of a panel of 189 informative SNPs, and demonstrate how these can reliably assign confiscated individuals to one of the management units established. Lastly, we assess hybridization between the Yellow cardinal and the Diuca finch (Diuca diuca), which is reported to occur in regions of sympatry. We confirm that hybridization occurs, although it is not as common as previously thought, and that hybrids might be fertile, as we found evidence of backcrossing with Yellow cardinals. We discuss the implications of this introgression for the evolution and conservation of Yellow cardinals. Our study provides new, valuable information that can guide conservation efforts, comprising a test case for the use of genomics in combating illegal trafficking, with potential application beyond the case of the Yellow cardinal.

The Andean and Atlantic forests are separated by the open vegetation corridor, which acts as a geographic barrier. However, these forests experimented cycles of connection and isolation in the past which shaped the phylogeographic patterns of their biotas. We analyzed the evolutionary history of the Rufous-capped Antshrike (Thamnophilus ruficapillus), a species with a disjunct distribution in the Atlantic and Andean forests and therefore an appropriate model to study the effect of the open vegetation corridor and the Andes on the diversification of the Neotropical avifauna. We performed a phylogenetic/phylogeographic analysis including the five subspecies, using mitochondrial and nuclear genomic DNA, and also studied their differences in vocalizations and plumage coloration. Both the mitochondrial and nuclear DNA evidenced a marked phylogeographic structure with three differentiated lineages that diverged without gene flow in the Pleistocene (1.0-1.7 million years ago): one in the Atlantic Forest and two in the Andean forest. However, the two Andean lineages do not coincide with the two disjunct areas of distribution of the species in the Andes. Vocalizations were significantly different between most subspecies, but their pattern of differentiation was discordant with that of the nuclear and mitochondrial DNA. In fact, there is no song differentiation between the subspecies of the Atlantic Forest and that of the northwestern Bolivian Andes, even though they differ genetically and belong to different lineages. Consistently, no differences were found in plumage coloration between the subspecies of the Atlantic Forest and that of the southern Andes. Our results suggest a complex evolutionary history in this species, which differentiated both due to dispersion across the open vegetation corridor, likely during a period of connection between the Andean and Atlantic forests, and as a consequence of a geographic barrier in northern Bolivia. In both cases Pleistocene climatic oscillations appear to have influenced the species diversification.