Unveiling the demographic history of three Malagasy amphibian species using ddRAD sequencing

Abstract

Madagascar is one of the largest islands in the world, hosting almost unparalleled levels of species richness and endemism. Its unique biodiversity is threatened by multiple factors (e.g. deforestation, overexploitation and invasive species), making it a critical priority region for international conservation efforts. In this study, we applied a double digest Rad sequencing (ddRADseq) approach to infer the demographic history and evolution of the effective population size (Ne) of three amphibian species - Ptychadena mascareniensis, Boophis obscurus and Mantidactylus bourgati - which cooccur in the region of the Andringitra Massif, in southeastern Madagascar. These species differ strongly in their distributional range sizes (from widespread throughout the country, to endemic to a portion of Madagascar, or microendemic to the Andringitra region, respectively). Since RAD-seq methods allow to produce cost-effective and informative representations of a species genome and do not necessarily require a reference genome to perform efficiently, they are suitable for studying non-model organisms. Therefore, we applied a ddRADseq approach to obtain genomic data for these target species and inferred past demographic trends, such as possible populations contractions, expansions and/or bottlenecks, and related them to the history of events that characterized the area surrounding our sampling sites. Our findings suggest that the Ne of Boophis obscurus and Mantidactylus bourgati have sharply decreased during a time period compatible with human expansion in Madagascar, possibly due to the reduction, fragmentation, or degradation of their suitable habitats. In contrast, Ptychadena mascareniensis experienced an increase in Ne during a similar timeframe, likely due to the expansion of open areas conducive to its habitat preferences. This study aimed to contribute to the conservation of these species by understanding their recent past demographic responses to past pressures, providing an idea of their potential reactions to future changes, and suggesting conservation strategies specifically tailored to their ecological needs.