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.

Fish ear bones, known as otoliths, are often collected by fisheries to assist in management, and are a common sample type in museum and national archives. Beyond their utility for aging, morphological and trace element analysis, otoliths are a repository of valuable genomic information. Previous work has shown that DNA can be extracted from the trace quantities of tissue remaining on the surface of otoliths, despite the fact that they are often stored dry at room temperature. However, much of this work has used reduced-representation sequencing methods in clean lab conditions, to achieve adequate yields of DNA, libraries, and ultimately single-nucleotide polymorphisms (SNPs). Here, we pioneer the use of small-scale (spike-in) sequencing to screen otolith samples prepared in regular molecular biology laboratories for contamination and quality levels, submitting for whole-genome resequencing only samples above a defined endogenous DNA threshold. Despite the typically low quality and quantity of DNA extracted from otoliths, we are able to produce whole-genome libraries and ultimately sets of filtered, unlinked and even adaptive SNPs of ample size for downstream uses in population, climate, and conservation genomics. By comparing with a set of tissue samples from the same species, we are able to highlight the quality and efficacy of otolith DNA samples from DNA extraction and library preparation, to bioinformatic preprocessing and SNP calling. We provide detailed schematics, protocols, and scripts of our approach, such that it can be adopted widely by the community, improving the use of otoliths as a source of valuable genomic data.

Maned Three-Toed Sloths (Xenarthra: Bradypodidae) are endemic to the highly fragmented Atlantic Forest of Brazil. Both species, known as Northern Maned Sloths (Bradypus torquatus Illiger, 1811) and Southern Maned Sloths (Bradypus crinitus Gray, 1850), exhibit disconnected populations across the distributions. Our study investigates the evolutionary and demographic trajectories of these two sloth lineages, utilizing whole-genome resequencing data compared against a high-quality genome assembly. Our analysis reveals that the Southern Maned Sloth exhibits lower genetic diversity and a smaller historical population size compared to the Northern Maned Sloth. These disparities likely stem from differing environmental and climatic historical changes along the Atlantic Forest distribution during the Pleistocene, which was characterized by greater climate stability and larger refugia areas in the north. Nonetheless, the northern population has experienced a fast increase in inbreeding levels in the last 20 years, in a region of Bahia State with extensive recent deforestation associated with livestock farming, agriculture, and urban development. In addition, the northern lineage presented a higher genetic load, which could imply higher fitness costs for this population if inbreeding patterns persist. Taken together, these results confirm the independent evolutionary paths of these two lineages and underscore the conservation challenges faced due to historical evolutionary events and current deforestation of the Atlantic Forest.