Genomic Signatures in Maned Three‐Toed Sloths From Ancient to Recent Environmental Changes in Brazil's Threatened Atlantic Forest

Environmental and climatic changes have shaped the evolutionary trajectories of natural populations, leaving genomic signatures that reflect how species respond to these shifts and their impacts on genetic health. While these insights are essential for unravelling evolutionary histories and informing conservation strategies, studies on Neotropical species remain largely underrepresented. Maned Three-Toed Sloths, endemic to the fragmented Atlantic Forest of Brazil, were recently reclassified into two distinct species: the Northern and Southern Maned Sloths. Our study investigates the genomic imprints left by ancient and recent environmental changes in the Atlantic Forest in these two sloth lineages, using whole-genome resequencing data. Our analysis reveals that the Southern Maned Sloth exhibits a smaller historical population size than the Northern Maned Sloth. This disparity likely stems from differing climatic changes along the Atlantic Forest distribution during the Pleistocene, characterised by greater climatic stability and larger refugia areas in the north. Consequently, the southern lineage presents a lower genetic diversity and higher overall inbreeding level. Nonetheless, the northern population has experienced a fast increase in inbreeding levels in the last few decades, likely associated with extensive recent deforestation in the northeast region of Bahia State. The distinct demographic trajectories also resulted in the northern lineage carrying a higher genetic load, implying higher fitness costs for this lineage if inbreeding persists. Together, our findings confirm the independent evolutionary paths of these two lineages and underscore the unique conservation challenges posed by both historical climatic changes and ongoing deforestation of the Atlantic Forest.