Integrating genomics and habitat surveys to uncover population structure and regeneration challenges in Adansonia suarezensis (Malvaceae)

Abstract Background and Aims Adansonia suarezensis, one of Madagascar’s six endemic baobab species, is currently classified as Endangered in the IUCN Red List and faces severe risks from habitat loss and climate change, and it is predicted to become extinct by 2080 if no conservation actions are taken. We combined population genomics with ecological surveys to assess the genetic diversity, population structure and regeneration dynamics of this species across representative sites. Methods We generated single nucleotide polymorphism (SNP) data from 118 mature individuals sampled across four sites using a target capture approach and evaluated genetic diversity, inbreeding and population structure. Ecological surveys were conducted at Mahory and Beantely, representing the two genetic clusters, to compare forest structure, floristic composition and regeneration dynamics. Vertebrate diversity was also recorded to assess its potential influence on regeneration. Key Results Population genomic analyses identified two moderately differentiated genetic groups, with Mahory clearly distinct from the northern localities. Pairwise FST values ranged from 0.054 to 0.133, all being statistically significant (P = 0.001). Despite low overall genetic diversity, no evidence of inbreeding was detected, consistent with bat-mediated cross-pollination. Ecological surveys revealed higher species richness, greater structural diversity and stronger regeneration signals in Mahory, especially in core zones, compared with Beantely. By contrast, regeneration in Beantely was weak, with few saplings and juveniles, despite relatively high adult densities. These differences probably reflect stronger edge effects, greater disturbance and lower animal diversity at Beantely, which may limit pollination and seed dispersal. Conclusions Our results demonstrate that A. suarezensis is structured into two genetic groups with low but significant differentiation and that regeneration failure is widespread, but most pronounced in degraded edge habitats. Conservation strategies should therefore prioritize the protection of core forest zones, safeguard pollinator and disperser communities, and reinforce natural regeneration through targeted restoration. By integrating genomic and ecological perspectives, this study provides essential guidance for the long-term conservation of A. suarezensis.