Landscape and Pleistocene refuges played a major role in shaping the population structure of endemic Atlantic Forest spiny rats Trinomys dimidiatus and Trinomys iheringi (Echymidae)

The Atlantic Forest has experienced a significant loss of its original vegetation, with more than 80% of the biome now comprising small and isolated fragments. To understand species distribution, it is crucial to comprehend the impact of fragmentation on species persistence within this biome. Previous phylogeographic inferences have indicated that Trinomys iheringi and T. dimidiatus are structured into two populations. In this study, we employed a more comprehensive database to re-examine the phylogeography and conduct a detailed analysis of the demographic history and population structure of two Trinomys species. The results indicate that T. dimidiatus is structured into at least three populations: Serra dos Órgãos, South Center of Serra do Mar, and North of Serra do Mar. In contrast, T. iheringi is highly structured into two populations: São Paulo and Ilha Grande. The demographic analysis indicated T. dimidiatus from Serra do Mar exhibited an expansionary trend during periods of reduced sea level with an optimal area reduction during LGM. In the past, T. iheringi presented the expansion of suitable areas onto the emerging continental shelf during the Last Glacial Maximum (LGM) but it did not impact the population's structure. The results suggest that retreat forest events during the Pleistocene and landscape factors were instrumental in shaping the population structure of the Trinomys species. Additionally, T. iheringi represents an entirely isolated island population exhibiting no gene flow, and analysis suggests the presence of a new microendemic species.