Abstract
Conservation under the global biodiversity crisis demands strategic prioritisation to maximise the impact of limited resources. Incorporating evolutionary history, an often-overlooked facet of biodiversity, alongside extinction risk can reveal priority species and regions that traditional approaches might miss. In South Africa, herpetofauna exhibit exceptionally high diversity and endemism across heterogeneous landscapes, yet contemporary metrics rarely incorporate evolutionary potential. Here, phylogenetic diversity (PD), phylogenetic endemism (PE), expected loss of PD (xPDL), and evolutionarily distinct and globally endangered (EDGE) metrics are quantified for all native amphibians and reptiles of South Africa. National-scale phylogenies were generated, and spatial patterns compared against null models to identify significant deviations. Extinction probabilities derived from IUCN Red List categories were applied to estimate the PD indicator and the EDGE index, as well as to generate an updated list of EDGE species for both clades. Results indicated the projected loss of ~6.5% of amphibian PD and ~5% of reptile PD over the next 50 years without intervention. The PD metrics demonstrated a decoupling between PD, PE, and species richness, and highlighted spatial distributions of amphibian xPDL coinciding with areas of high PE. Building on these findings, PD and PE were intersected with national Protected Area (PA) networks, Key Biodiversity Areas (KBAs), and land-use data to evaluate conservation coverage, threats, and priorities. Most provinces are failing to protect 50% of the extent of heightened PD or PE zones, with the highest coverage in the Western Cape and Mpumalanga provinces. Complementarity analyses identified the fewest KBAs needed to optimise phylogenetic protection, highlighting iSimangaliso as the single most important KBA for PD, PE, and xPDL, with only four additional sites required to conserve over 80% of South Africa’s herpetofaunal PD. KwaZulu-Natal and the Western Cape were revealed as major hotspots for phylogenetic diversity and anthropogenic pressure, driven primarily by cultivation and plantations in both the grassland and fynbos biomes. Finally, the human-impacted phylogenetic endemism (HIPE) index further confirmed spatial congruence in priority areas across both clades. Integrating evolutionary metrics with extinction risk and landscape pressures revealed spatial conservation priorities and priority species, aligning with global monitoring frameworks, and guiding policy makers towards the preservation of South Africa’s unique herpetofaunal heritage.